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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pyfaidx">Debian Med / python-pyfaidx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280">dc77492a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T15:12:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.4</pre>
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<h4>22 changed files:</h4>
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#8871c02d740f4cad328693eef9ec41d8a509a416">
dev-requirements.txt
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<li class="file-stats">
<a href="#83b1dda3455005121b48aadc1fefedc1b5e999ea">
pyfaidx/__init__.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#30a91905c06a1f55fe48303cee6e6036da0c85b7">
tests/data/download_gene_fasta.py
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<li class="file-stats">
<a href="#e805f7df64ccdcc7314257ec4a439be10b25e551">
tests/test_FastaRecord.py
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<li class="file-stats">
<a href="#dc267182a4c117aac477ed6b399b8efef3846448">
tests/test_FastaRecord_iter.py
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<li class="file-stats">
<a href="#e4acef92bcc4812a5bd4040182e865cd01bd778b">
tests/test_FastaVariant.py
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<li class="file-stats">
<a href="#9dc5954fef27b8acacceef72246051841767d0b0">
tests/test_Fasta_bgzip.py
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<li class="file-stats">
<a href="#4a70750de4ebd92830820600ccee6861ea6d295d">
tests/test_Fasta_integer_index.py
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<li class="file-stats">
<a href="#d1e4f5f56e67f5dbaa8a221079b8301736ae2f5e">
tests/test_Fasta_synchronization.py
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<li class="file-stats">
<a href="#9e3cf9856497d9ff349afc7c8c50c5bb1c71a868">
tests/test_bio_seqio.py
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<li class="file-stats">
<a href="#8dfa9e6b648ed40ba1bc812642cf5a886f2c7b03">
tests/test_faidx.py
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<li class="file-stats">
<a href="#a222b1e8057a77c62c76a9361c638233eacbd151">
tests/test_feature_bounds_check.py
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<li class="file-stats">
<a href="#6f714b56ba3f46a151ee2b91022a458fd9c8e6e5">
tests/test_feature_default_seq.py
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<li class="file-stats">
<a href="#0d3f0a3598baee5caaf42b338be8317f0edf4902">
tests/test_feature_indexing.py
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<li class="file-stats">
<a href="#64ec433b3b32854e3f3ada287ab6ea004569952d">
tests/test_feature_key_function.py
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<li class="file-stats">
<a href="#562f427754839d2bd05384aefeb4ddf62625a252">
tests/test_feature_read_ahead_buffer.py
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<li class="file-stats">
<a href="#a9dc155009e92209186db2d9aa87b3ffecc98644">
tests/test_feature_sequence_as_raw.py
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<li class="file-stats">
<a href="#4c32d79098dfd4a5964f9258d84c3e5152b387b2">
tests/test_feature_spliced_seq.py
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<li class="file-stats">
<a href="#7eaf1cf32558b6c04e3d6d91f5123a1cf5adfa59">
tests/test_feature_split_char.py
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<li class="file-stats">
<a href="#918f1a692b59c81cf124edb2f54a5d18717f080e">
tests/test_sequence_class.py
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<h4>Changes:</h4>
<li id="561b88e19de321ca62c7590bbb350765fb110905">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">|<span class="idiff left right">Travis</span>| |PyPI| |Coverage| |Depsy|</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">|<span class="idiff left right">CI| |Package</span>| |PyPI| |Coverage| |Depsy|</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Description</span>
</pre>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">-----------</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +26,7 @@ If you use pyfaidx in your publication, please cite:</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Installation</span>
</pre>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">------------</span>
</pre>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">This package is tested under Linux<span class="idiff left right">, MacOS, and Windows using Python 3.2-3.4, 2.7, 2.6, and pypy</span> and is available from the PyPI:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">This package is tested under Linux<span class="idiff left right"> and macOS using Python 3.6+, and</span> and is available from the PyPI:</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,7 @@ or download a `release <https://github.com/mdshw5/pyfaidx/releases>`_ and:</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> python setup.py install</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">If using ``pip install --user`` make sure to add ``/home/$<span class="idiff left right">(whoami)</span>/.local/bin`` to your ``$PATH`` if you want to run the ``faidx`` script.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">If using ``pip install --user`` make sure to add ``/home/$<span class="idiff left">USER</span>/.local/bin`` to your ``$PATH`` <span class="idiff right">(on linux) or ``/Users/$USER/Library/Python/{python version}/bin`` (on macOS) </span>if you want to run the ``faidx`` script.</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Usage</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">-----</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -575,13 +575,16 @@ create also the relevant test.</td>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="plaintext">To get test running on your machine:</span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="plaintext"> - Create a new virtualenv and install the `dev-requirements.txt`.</span>
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext"> pip install -r dev-requirements.txt</span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="plaintext"> - Download the test data running:</span>
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="plaintext"> python tests/data/download_gene_fasta.py</span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="plaintext"> - Run the tests with</span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="plaintext"> <span class="idiff left">nose</span>tests<span class="idiff right"> --with-coverage --cover-package=pyfaidx</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext"> <span class="idiff left right">py</span>tests</span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="plaintext">Acknowledgements</span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="plaintext">----------------</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -595,6 +598,9 @@ Comprehensive Cancer Center in the Department of Oncology.</td>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="plaintext">.. |Travis| image:: https://travis-ci.com/mdshw5/pyfaidx.svg?branch=master</span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="plaintext"> :target: https://travis-ci.com/mdshw5/pyfaidx</span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext">.. |CI| image:: https://github.com/mdshw5/pyfaidx/actions/workflows/main.yml/badge.svg?branch=master</span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext"> :target: https://github.com/mdshw5/pyfaidx/actions/workflows/main.yml</span>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="plaintext">.. |PyPI| image:: https://img.shields.io/pypi/v/pyfaidx.svg?branch=master</span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="plaintext"> :target: https://pypi.python.org/pypi/pyfaidx</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -611,3 +617,6 @@ Comprehensive Cancer Center in the Department of Oncology.</td>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="plaintext">.. |Appveyor| image:: https://ci.appveyor.com/api/projects/status/80ihlw30a003596w?svg=true</span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="plaintext"> :target: https://ci.appveyor.com/project/mdshw5/pyfaidx</span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext">.. |Package| image:: https://github.com/mdshw5/pyfaidx/actions/workflows/pypi.yml/badge.svg</span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext"> :target: https://github.com/mdshw5/pyfaidx/actions/workflows/pypi.yml</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#8871c02d740f4cad328693eef9ec41d8a509a416"><strong>dev-requirements.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/six" rel="nofollow noreferrer noopener" target="_blank">six</a></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/nose" rel="nofollow noreferrer noopener" target="_blank">nose</a></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pytest" rel="nofollow noreferrer noopener" target="_blank">pytest</a></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pytest-cov" rel="nofollow noreferrer noopener" target="_blank">pytest-cov</a></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/setuptools" rel="nofollow noreferrer noopener" target="_blank">setuptools</a></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/mock" rel="nofollow noreferrer noopener" target="_blank">mock</a></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/cython" rel="nofollow noreferrer noopener" target="_blank">cython</a> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pysam" rel="nofollow noreferrer noopener" target="_blank">pysam</a> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/requests" rel="nofollow noreferrer noopener" target="_blank">requests</a> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/coverage" rel="nofollow noreferrer noopener" target="_blank">coverage</a> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pyfasta" rel="nofollow noreferrer noopener" target="_blank">pyfasta</a> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pyvcf" rel="nofollow noreferrer noopener" target="_blank">pyvcf</a> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/numpy" rel="nofollow noreferrer noopener" target="_blank">numpy</a> </span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biopython" rel="nofollow noreferrer noopener" target="_blank">biopython</a></span></pre>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/setuptools" rel="nofollow noreferrer noopener" target="_blank">setuptools</a> >= 0.7</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/mock" rel="nofollow noreferrer noopener" target="_blank">mock</a>; python_version < '3.3'</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#83b1dda3455005121b48aadc1fefedc1b5e999ea"><strong>pyfaidx/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,6 +16,7 @@ from itertools import islice</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">math</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ceil</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">getmtime</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">threading</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Lock</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pkg_resources</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_distribution</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PY2</span><span class="p">,</span> <span class="n" style="color: #333;">PY3</span><span class="p">,</span> <span class="n" style="color: #333;">integer_types</span><span class="p">,</span> <span class="n" style="color: #333;">string_types</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six.moves</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">zip_longest</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,15 +25,14 @@ try:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrderedDict</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#python 2.6</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ordereddict</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrderedDict</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_distribution</span><span class="p">(</span><span class="s" style="color: #d14;">"pyfaidx"</span><span class="p">).</span><span class="n" style="color: #333;">version</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="nb" style="color: #0086b3;">buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">memoryview</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="n" style="color: #333;">dna_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.6.2'</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">KeyFunctionError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"""Raised if the key_function argument is invalid."""</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,6 +45,10 @@ class IndexNotFoundError(IOError):</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"""Raised if read_fai cannot open the index file."""</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VcfIndexNotFoundError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"""Raised if vcf cannot find a tbi file."""</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaNotFoundError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"""Raised if the fasta file cannot be opened."""</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -348,8 +352,8 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bgzf</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">bgzf_version</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;"><span class="idiff left">distutils</span>.version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff right">Loose</span>Version</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">Loose</span>Version</span><span class="p">(</span><span class="n" style="color: #333;">bgzf_version</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff right">Loose</span>Version</span><span class="p">(</span><span class="s" style="color: #d14;">'1.73'</span><span class="p">):</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;"><span class="idiff left right">packaging</span>.version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Version</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Version</span><span class="p">(</span><span class="n" style="color: #333;">bgzf_version</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Version</span><span class="p">(</span><span class="s" style="color: #d14;">'1.73'</span><span class="p">):</span></span>
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353
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ImportError</span></span>
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354
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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355
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1130,6 +1134,8 @@ class FastaVariant(Fasta):</td>
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1130
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">Reader</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">vcf_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1131
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1132
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1136
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<pre style="margin: 0;"> <span id="LC1136" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">"File {0} does not exist."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">vcf_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">vcf_file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tbi'</span><span class="p">):</span></span>
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1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">VcfIndexNotFoundError</span><span class="p">(</span><span class="s" style="color: #d14;">"File {0} has not tabix index."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">vcf_file</span><span class="p">))</span></span>
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1133
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1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1134
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span></span>
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1135
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1163,14 +1169,24 @@ class FastaVariant(Fasta):</td>
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1163
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1169
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<pre style="margin: 0;"> <span id="LC1169" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1164
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="python"> <span class="n" style="color: #333;">seq_mut</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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1165
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1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>
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1166
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<pre style="margin: 0;">-<span id="LC1166" class="line" lang="python"> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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1167
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<pre style="margin: 0;">-<span id="LC1167" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">var</span><span class="p">:</span></span>
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1168
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<pre style="margin: 0;">-<span id="LC1168" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">is_snp</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># skip indels</span></span>
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1169
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<pre style="margin: 0;">-<span id="LC1169" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sample</span><span class="p">)</span></span>
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1170
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<pre style="margin: 0;">-<span id="LC1170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">gt_type</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gt_type</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">eval</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">):</span></span>
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1171
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<pre style="margin: 0;">-<span id="LC1171" class="line" lang="python"> <span class="n" style="color: #333;">alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">ALT</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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1172
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<pre style="margin: 0;">-<span id="LC1172" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1173
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<pre style="margin: 0;">-<span id="LC1173" class="line" lang="python"> <span class="n" style="color: #333;">seq_mut</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">)</span></span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="python"> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">var</span><span class="p">:</span></span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">is_snp</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># skip indels</span></span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sample</span><span class="p">)</span></span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">gt_type</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gt_type</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">eval</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">):</span></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="python"> <span class="n" style="color: #333;">alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">ALT</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="python"> <span class="n" style="color: #333;">seq_mut</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">)</span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Can be raised if name is not part of tabix for vcf</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">_tabix</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">_tabix</span><span class="p">.</span><span class="n" style="color: #333;">contigs</span><span class="p">:</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The chromosome name is not part of the vcf</span></span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The sequence returned is the same as the reference</span></span>
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This is something else</span></span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">e</span></span>
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1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="python"></span>
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1190
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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># slice the list in case we added an MNP in last position</span></span>
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1175
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1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">as_raw</span><span class="p">:</span></span>
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1176
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1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">seq_mut</span><span class="p">[:</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,19 +6,9 @@ install_requires = ['six', 'setuptools >= 0.7']</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">'ordereddict'</span><span class="p">,</span> <span class="s" style="color: #d14;">'argparse'</span><span class="p">])</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_version</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="s" style="color: #d14;">""" Parse the version number variable __version__ from a script. """</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">version_re</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">r</span><span class="s" style="color: #d14;">"^__version__ = ['\"]([^'\"]*)['\"]"</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">version_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">version_re</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">M</span><span class="p">).</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">version_str</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'pyfaidx'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">provides</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'pyfaidx'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_version</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'pyfaidx/__init__.py'</span><span class="p">,</span> <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()),</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Matthew Shirley'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'mdshw5@gmail.com'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'http://mattshirley.com'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +18,8 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'BSD'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'pyfaidx'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">install_requires</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">use_scm_version</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"local_scheme"</span><span class="p">:</span> <span class="s" style="color: #d14;">"no-local-version"</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'setuptools_scm'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'faidx = pyfaidx.cli:main'</span><span class="p">]},</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 5 - Production/Stable"</span><span class="p">,</span></span>
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<li id="30a91905c06a1f55fe48303cee6e6036da0c85b7">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#30a91905c06a1f55fe48303cee6e6036da0c85b7"><strong>tests/data/download_gene_fasta.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,21 +36,30 @@ def fetch_genes(filename, suffix=None):</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch_chr22</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">requests</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">io</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">requests</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/technical/reference/human_b36_male.fa.gz'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">compressed</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="n" style="color: #333;">GzipFile</span><span class="p">(</span><span class="n" style="color: #333;">fileobj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">compressed</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">raw</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gz</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="n" style="color: #333;">GzipFile</span><span class="p">(</span><span class="n" style="color: #333;">fileobj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">io</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">BytesIO</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">compressed</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff">content</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">gz</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">chr22</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gz</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>22'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">line_content</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line_content</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>22'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line_content</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">chr22</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">chr22</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">chr22</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">curl</span><span class="p">.</span><span class="n" style="color: #333;">kill</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">chr22</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line_content</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">chr22</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line_content</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_fake_chr</span><span class="p">(</span><span class="n" style="color: #333;">existing_fasta</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">existing_fasta</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">old_fa</span><span class="p">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">old_fa</span><span class="p">:</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'>fake chromosome not in vcf</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'ATCG</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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54
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fake_chr22</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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56
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fake up some data """</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,10 +93,16 @@ if __name__ == "__main__":</td>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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85
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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86
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="s" style="color: #d14;">"genes.fasta"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="s" style="color: #d14;">"genes.fasta.lower"</span><span class="p">):</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"GETTING genes"</span><span class="p">)</span></span>
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87
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">fetch_genes</span><span class="p">(</span><span class="s" style="color: #d14;">"genes.fasta"</span><span class="p">)</span></span>
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88
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="s" style="color: #d14;">"chr22.vcf.gz"</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"GETTING vcf"</span><span class="p">)</span></span>
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89
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">fetch_chr22_vcf</span><span class="p">(</span><span class="s" style="color: #d14;">"chr22.vcf.gz"</span><span class="p">)</span></span>
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90
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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="s" style="color: #d14;">"chr22.fasta"</span><span class="p">):</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"GETTING chr22.fasta"</span><span class="p">)</span></span>
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91
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">fetch_chr22</span><span class="p">(</span><span class="s" style="color: #d14;">"chr22.fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="s" style="color: #d14;">"chr22andfake.fasta"</span><span class="p">):</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"adding fake chr"</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">add_fake_chr</span><span class="p">(</span><span class="s" style="color: #d14;">"chr22.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"chr22andfake.fasta"</span><span class="p">)</span></span>
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92
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">bgzip_compress_fasta</span><span class="p">(</span><span class="s" style="color: #d14;">"genes.fasta"</span><span class="p">)</span></span>
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93
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">bgzip_compress_fasta</span><span class="p">(</span><span class="s" style="color: #d14;">"chr22.fasta"</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#e805f7df64ccdcc7314257ec4a439be10b25e551"><strong>tests/test_FastaRecord.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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3
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Fasta</span></span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NamedTemporaryFile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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7
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">difflib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Differ</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFastaRecord</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sequence_uppercase</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test that the sequence is always returned in</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> uppercase, even if it is in lowercase in the</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"> reference genome.</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/genes.fasta.lower"</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">reference_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_always_upper</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">reference_normal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.lower.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">reference_upper</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">reference_normal</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_long_names</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test that deflines extracted using FastaRecord.long_name are</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> identical to deflines in the actual file.</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sequence_uppercase</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test that the sequence is always returned in</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> uppercase, even if it is in lowercase in the</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> reference genome.</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/genes.fasta.lower"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">reference_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_always_upper</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">reference_normal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.lower.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">reference_upper</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">reference_normal</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_long_names</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test that deflines extracted using FastaRecord.long_name are</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> identical to deflines in the actual file.</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">long_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">deflines</span><span class="p">,</span> <span class="n" style="color: #333;">long_names</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">long_names</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_62</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">""" Check for pathogenic FastaRecord.long_name behavior in mdshw5/pyfaidx#62 """</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">long_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">deflines</span><span class="p">,</span> <span class="n" style="color: #333;">long_names</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">long_names</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_62</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">""" Check for pathogenic FastaRecord.long_name behavior in mdshw5/pyfaidx#62 """</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">))</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line_len</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">):</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="sa">b</span><span class="s" style="color: #d14;">'N'</span> <span class="o" style="font-weight: 600;">*</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="sa">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">long_name</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa'</span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa.fai'</span><span class="p">)</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">writelines</span><span class="p">(</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">Differ</span><span class="p">().</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">deflines</span><span class="p">,</span> <span class="n" style="color: #333;">long_names</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">long_names</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_unpadded_length</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/padded.fasta"</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">padded</span><span class="p">:</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">test_padded</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">80</span><span class="p">)</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">30</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"A"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">20</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">30</span><span class="p">)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'ascii'</span><span class="p">))</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line_len</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">></span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">):</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="sa">b</span><span class="s" style="color: #d14;">'N'</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="sa">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">fasta_uniform_len</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">long_name</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa'</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_62.fa.fai'</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">writelines</span><span class="p">(</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">Differ</span><span class="p">().</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">deflines</span><span class="p">,</span> <span class="n" style="color: #333;">long_names</span><span class="p">)))</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">long_names</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_unpadded_length</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/padded.fasta"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">padded</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">test_padded</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">80</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">30</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"A"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">20</span><span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">30</span><span class="p">)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">80</span><span class="p">)</span></span>
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92
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"N"</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">80</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">padded</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">"test_padded"</span><span class="p">].</span><span class="n" style="color: #333;">unpadded_len</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/padded.fasta'</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/padded.fasta.fai'</span><span class="p">)</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_numpy_array</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test the __array_interface__ """</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/genes.fasta.lower"</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">np_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">asarray</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">np_array</span><span class="p">,</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestMutableFastaRecord</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mutable</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mutable_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta.fai'</span><span class="p">)</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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133
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_fasta_to_same</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">"test_padded"</span><span class="p">].</span><span class="n" style="color: #333;">unpadded_len</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/padded.fasta'</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/padded.fasta.fai'</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_numpy_array</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test the __array_interface__ """</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/genes.fasta.lower"</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">np_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">asarray</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">np_array</span><span class="p">,</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index_mutable</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mutable</span><span class="p">:</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">mutable_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta.fai'</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_fasta_to_same</span><span class="p">(</span><span class="n" style="color: #333;">remove_index_mutable</span><span class="p">):</span></span>
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135
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,26 +133,26 @@ class TestMutableFastaRecord(TestCase):</td>
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139
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">])</span></span>
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141
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_fasta_to_N</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_fasta_to_N</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index_mutable</span></span><span class="p">):</span></span>
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143
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">'N'</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span></span>
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146
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mutable</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chunk</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_single_position</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_single_position</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index_mutable</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'N'</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mutable</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chunk</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p"><span class="idiff left right">(</span></span><span class="nb" style="color: #0086b3;">TypeError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_immutable_fasta</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mark</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xfail</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="nb" style="color: #0086b3;">TypeError</span><span class="p">)</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_immutable_fasta</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index_mutable</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">'N'</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p"><span class="idiff left right">(</span></span><span class="nb" style="color: #0086b3;">IOError</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_too_long</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mark</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xfail</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="nb" style="color: #0086b3;">IOError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutate_too_long</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index_mutable</span></span><span class="p">):</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes_mutable.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">101</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">'N'</span></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">mutable</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#dc267182a4c117aac477ed6b399b8efef3846448"><strong>tests/test_FastaRecord_iter.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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2
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Fasta</span></span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFastaRecordIter</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_fasta</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))))</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_<span class="idiff">fetch_whole_fasta</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">expect</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'>'</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chain</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">([</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Fasta</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'data/genes.fasta'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">as_raw</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff right">))))</span></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;"><span class="idiff left">expect</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">result</span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_<span class="idiff left">line_len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">remove_index</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">fasta</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Fasta</span></span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">next</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">iter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">)))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">faidx</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">lenc</span></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_line_len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">lenc</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reverse_iter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="n" style="color: #333;">line</span><span class="p">[::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">][::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))))</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">reversed</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))))</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span></pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reverse_iter</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="n" style="color: #333;">line</span><span class="p">[::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">][::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))))</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">reversed</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#e4acef92bcc4812a5bd4040182e865cd01bd778b"><strong>tests/test_FastaVariant.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">,</span> <span class="n" style="color: #333;">Fasta</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.plugins.skip</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFastaVariant</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_variant</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="idiff left right"> </span><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32330458</span><span class="p">:</span><span class="mi" style="color: #099;">32330462</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGG'</span> <span class="c1" style="color: #998; font-style: italic;"># het</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32352282</span><span class="p">:</span><span class="mi" style="color: #099;">32352286</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGC'</span> <span class="c1" style="color: #998; font-style: italic;"># hom</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">raise</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SkipTest</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_variant</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32330458</span><span class="p">:</span><span class="mi" style="color: #099;">32330462</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGG'</span> <span class="c1" style="color: #998; font-style: italic;"># het</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32352282</span><span class="p">:</span><span class="mi" style="color: #099;">32352286</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGC'</span> <span class="c1" style="color: #998; font-style: italic;"># hom</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">skip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"pysam not installed."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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29
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_hom_variant</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="idiff left right"> </span><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32330458</span><span class="p">:</span><span class="mi" style="color: #099;">32330462</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CGGG'</span> <span class="c1" style="color: #998; font-style: italic;"># het</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32352282</span><span class="p">:</span><span class="mi" style="color: #099;">32352286</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGC'</span> <span class="c1" style="color: #998; font-style: italic;"># hom</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">raise</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SkipTest</span></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_hom_variant</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32330458</span><span class="p">:</span><span class="mi" style="color: #099;">32330462</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CGGG'</span> <span class="c1" style="color: #998; font-style: italic;"># het</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32352282</span><span class="p">:</span><span class="mi" style="color: #099;">32352286</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGC'</span> <span class="c1" style="color: #998; font-style: italic;"># hom</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">skip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"pysam not installed."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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38
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_het_variant</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="idiff left right"> </span><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32330458</span><span class="p">:</span><span class="mi" style="color: #099;">32330462</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGG'</span> <span class="c1" style="color: #998; font-style: italic;"># het</span></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32352282</span><span class="p">:</span><span class="mi" style="color: #099;">32352286</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CGGC'</span> <span class="c1" style="color: #998; font-style: italic;"># hom</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">raise</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SkipTest</span></span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_het_variant</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32330458</span><span class="p">:</span><span class="mi" style="color: #099;">32330462</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CAGG'</span> <span class="c1" style="color: #998; font-style: italic;"># het</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="mi" style="color: #099;">32352282</span><span class="p">:</span><span class="mi" style="color: #099;">32352286</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'CGGC'</span> <span class="c1" style="color: #998; font-style: italic;"># hom</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">skip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"pysam not installed."</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_pos</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">].</span><span class="n" style="color: #333;">variant_sites</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">16042793</span><span class="p">,</span> <span class="mi" style="color: #099;">21833121</span><span class="p">,</span> <span class="mi" style="color: #099;">29153196</span><span class="p">,</span> <span class="mi" style="color: #099;">29187373</span><span class="p">,</span> <span class="mi" style="color: #099;">29187448</span><span class="p">,</span> <span class="mi" style="color: #099;">29194610</span><span class="p">,</span> <span class="mi" style="color: #099;">29821295</span><span class="p">,</span> <span class="mi" style="color: #099;">29821332</span><span class="p">,</span> <span class="mi" style="color: #099;">29993842</span><span class="p">,</span> <span class="mi" style="color: #099;">32330460</span><span class="p">,</span> <span class="mi" style="color: #099;">32352284</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_chr_not_in_vcf</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22andfake.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'fake'</span><span class="p">][:</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ATCG'</span> <span class="c1" style="color: #998; font-style: italic;"># fake is not in vcf </span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="s" style="color: #d14;">"pysam not installed."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_pos</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">].</span><span class="n" style="color: #333;">variant_sites</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">16042793</span><span class="p">,</span> <span class="mi" style="color: #099;">21833121</span><span class="p">,</span> <span class="mi" style="color: #099;">29153196</span><span class="p">,</span> <span class="mi" style="color: #099;">29187373</span><span class="p">,</span> <span class="mi" style="color: #099;">29187448</span><span class="p">,</span> <span class="mi" style="color: #099;">29194610</span><span class="p">,</span> <span class="mi" style="color: #099;">29821295</span><span class="p">,</span> <span class="mi" style="color: #099;">29821332</span><span class="p">,</span> <span class="mi" style="color: #099;">29993842</span><span class="p">,</span> <span class="mi" style="color: #099;">32330460</span><span class="p">,</span> <span class="mi" style="color: #099;">32352284</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="s" style="color: #d14;">"pysam not installed."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_diff</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">print</span><span class="p">([(</span><span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">].</span><span class="n" style="color: #333;">variant_sites</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">].</span><span class="n" style="color: #333;">variant_sites</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">raise</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SkipTest</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_all_diff</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">remove_index</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FastaVariant</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/chr22.vcf.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">het</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr22.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">([(</span><span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">].</span><span class="n" style="color: #333;">variant_sites</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'22'</span><span class="p">].</span><span class="n" style="color: #333;">variant_sites</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">skip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"pysam not installed."</span></span><span class="p"><span class="idiff right">)</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#9dc5954fef27b8acacceef72246051841767d0b0"><strong>tests/test_Fasta_bgzip.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Fasta</span><span class="p">,</span> <span class="n" style="color: #333;">Faidx</span><span class="p">,</span> <span class="n" style="color: #333;">UnsupportedCompressionFormat</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span></span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span><span class="p">,</span> <span class="n" style="color: #333;">expectedFailure</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.plugins.skip</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SkipTest</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">expectedFailure</span> <span class="c1" style="color: #998; font-style: italic;"># python2.6</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.plugins.skip</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestIndexing</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">expectedFailure</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_126</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">""" Samtools BGZF index should be identical to pyfaidx BGZF index """</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1| 3510 114 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1| 481 3789 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1| 642 4368 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1| 4573 5141 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212.1| 5374 15415 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583788|ref|NM_001282545.1| 4170 20980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583786|ref|NM_001282543.1| 5466 25324 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583785|ref|NM_000465.3| 5523 30980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583740|ref|NM_001282549.1| 3984 36696 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583738|ref|NM_001282548.1| 4113 40851 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373237|ref|XM_005265508.1| 2794 57830 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507.1| 2848 60824 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081.1| 1009 63849 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080.1| 4884 65009 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1| 2819 70099 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFastaBGZF</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_slice</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_index</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_fasta</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))))</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_line_len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">lenc</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">UnsupportedCompressionFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutable_bgzf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">)</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_long_names</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test that deflines extracted using FastaRecord.long_name are</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> identical to deflines in the actual file.</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>'</span><span class="p">:</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">long_name</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">long_names</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_entry</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'ATGACATCATTTTCCACCTCTGCTCAGTGTTCAACATCTGA'</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="s" style="color: #d14;">'CAGTGCTTGCAGGATCTCTCCTGGACAAATCAATCAGGTACGACCA'</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="s" style="color: #d14;">'AAACTGCCGCTTTTGAAGATTTTGCATGCAGCAGGTGCGCAAGG'</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">'TGAAATGTTCACTGTTAAAGAGGTCATGCACTATTTAGGTCAGTACAT'</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">'AATGGTGAAGCAACTTTATGATCAGCAGGAGCAGCATATGGTATATTG'</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">'TGGTGGAGATCTTTTGGGAGAACTACTGGGACGTCAGAGCTTCTCCGTG'</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">'AAAGACCCAAGCCCTCTCTATGATATGCTAAGAAAGAATCTTGTCACTTT'</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">'AGCCACTGCTACTACAGCAAAGTGCAGAGGAAAGTTCCACTTCCAGAAAAA'</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">'GAACTACAGAAGACGATATCCCCACACTGCCTACCTCAGAGCATAAATGCA'</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">'TACATTCTAGAGAAGGTGATTGAAGTGGGAAAAAATGATGACCTGGAGGACTC'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_middle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_end</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rev</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GA'</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_past_bounds</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">5000</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_negative</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_reversed_coordinates</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_keyerror</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch a key that does not exist """</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|joe|gb|KF435150.1|'</span><span class="p">,</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_blank_string</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="s" style="color: #d14;">""" seq[0:0] should return a blank string mdshw5/pyfaidx#53 """</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_beginning</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ATGA'</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_end</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">:]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACTC'</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_start</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_consistency</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_faidx</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
210
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
211
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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<td class="old_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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<td class="old_line diff-line-num old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_fasta</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">))</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">101</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_negate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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231
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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232
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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233
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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234
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">101</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false_negate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border_padded</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">default_seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TCNNNNNNNNNNNNNNNNNNN'</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span></pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">bio</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">bio</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz.fai'</span><span class="p">)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">bio</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Biopython is not installed."</span><span class="p">)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_126</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">""" Samtools BGZF index should be identical to pyfaidx BGZF index """</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1| 3510 114 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1| 481 3789 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1| 642 4368 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1| 4573 5141 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215.1| 5317 9901 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212.1| 5374 15415 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583788|ref|NM_001282545.1| 4170 20980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583786|ref|NM_001282543.1| 5466 25324 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583785|ref|NM_000465.3| 5523 30980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583740|ref|NM_001282549.1| 3984 36696 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583738|ref|NM_001282548.1| 4113 40851 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384540|ref|XM_005249645.1| 2752 45151 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384538|ref|XM_005249644.1| 3004 48071 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384536|ref|XM_005249643.1| 3109 51246 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384534|ref|XM_005249642.1| 3097 54528 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373237|ref|XM_005265508.1| 2794 57830 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507.1| 2848 60824 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081.1| 1009 63849 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080.1| 4884 65009 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1| 2819 70099 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_slice</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_index</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_fasta</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">([</span><span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">))))</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_line_len</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">lenc</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">UnsupportedCompressionFormat</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_mutable_bgzf</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">mutable</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_long_names</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test that deflines extracted using FastaRecord.long_name are</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> identical to deflines in the actual file.</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'>'</span><span class="p">:</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">deflines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">long_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">long_name</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">deflines</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">long_names</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_entry</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'ATGACATCATTTTCCACCTCTGCTCAGTGTTCAACATCTGA'</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">'CAGTGCTTGCAGGATCTCTCCTGGACAAATCAATCAGGTACGACCA'</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="s" style="color: #d14;">'AAACTGCCGCTTTTGAAGATTTTGCATGCAGCAGGTGCGCAAGG'</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">'TGAAATGTTCACTGTTAAAGAGGTCATGCACTATTTAGGTCAGTACAT'</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">'AATGGTGAAGCAACTTTATGATCAGCAGGAGCAGCATATGGTATATTG'</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="s" style="color: #d14;">'TGGTGGAGATCTTTTGGGAGAACTACTGGGACGTCAGAGCTTCTCCGTG'</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">'AAAGACCCAAGCCCTCTCTATGATATGCTAAGAAAGAATCTTGTCACTTT'</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">'AGCCACTGCTACTACAGCAAAGTGCAGAGGAAAGTTCCACTTCCAGAAAAA'</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">'GAACTACAGAAGACGATATCCCCACACTGCCTACCTCAGAGCATAAATGCA'</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">'TACATTCTAGAGAAGGTGATTGAAGTGGGAAAAAATGATGACCTGGAGGACTC'</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_middle</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_end</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rev</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GA'</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_past_bounds</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">5000</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_negative</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_reversed_coordinates</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_keyerror</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch a key that does not exist """</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|joe|gb|KF435150.1|'</span><span class="p">,</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_blank_string</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="s" style="color: #d14;">""" seq[0:0] should return a blank string mdshw5/pyfaidx#53 """</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_beginning</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ATGA'</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_end</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">:]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACTC'</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_start</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_consistency</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_faidx</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_fasta</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">))</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">101</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_negate</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">101</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false_negate</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border_padded</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.gz'</span><span class="p">,</span> <span class="n" style="color: #333;">default_seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TCNNNNNNNNNNNNNNNNNNN'</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#4a70750de4ebd92830820600ccee6861ea6d295d"><strong>tests/test_Fasta_integer_index.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Fasta</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFastaIntIndex</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_slice</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_slice</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][:</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_index</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span></pre>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_index</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|563317589|dbj|AB821309.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#d1e4f5f56e67f5dbaa8a221079b8301736ae2f5e"><strong>tests/test_Fasta_synchronization.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrderedDict</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#python 2.6</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +22,7 @@ class _ThreadReadSequence(threading.Thread):</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">sub_seq_slices</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">slice</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">seq_len</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">sub_seq_slices</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rand</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">random</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">sub_seq_slices</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">result_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result_map</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">result_lock</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result_lock</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +52,7 @@ class _ThreadWriteSequence(threading.Thread):</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">sub_seq_slices</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">slice</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">seq_len</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">sub_seq_slices</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rand</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">random</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">shuffle</span><span class="p">(</span><span class="n" style="color: #333;">sub_seq_slices</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span></span>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#9e3cf9856497d9ff349afc7c8c50c5bb1c71a868"><strong>tests/test_bio_seqio.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Fasta</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.plugins.skip</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Skip</span><span class="p">,</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">test_bio</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">test_bio</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestBioSeqIO</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">bio</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">bio</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_entry</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test_bio</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">"rU"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">bio</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Biopython is not installed."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_entry</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_whole_entry</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test_bio</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">"rU"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">[::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">bio</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Biopython is not installed."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_whole_entry</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">[::</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_revcomp_whole_entry</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test_bio</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">"rU"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][:].</span><span class="n" style="color: #333;">reverse</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">().</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span></pre>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">bio</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Biopython is not installed."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_revcomp_whole_entry</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][:].</span><span class="n" style="color: #333;">reverse</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqio</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">].</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">().</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#8dfa9e6b648ed40ba1bc812642cf5a886f2c7b03"><strong>tests/test_faidx.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">filecmp</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">,</span> <span class="n" style="color: #333;">BedError</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BedError</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx.cli</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NamedTemporaryFile</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestCLI</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">BedError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_short_line_lengths</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bed'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/malformed.bed'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_split_entry</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--split-files'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">'gi557361099gbKF435150.1.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'gi557361099gbKF435150.1.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|:1-1000'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_warning</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'foo'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_auto_strand</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test that --auto-strand produces the same output as --reverse --complement"""</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">auto_strand</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">noto_strand</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--auto-strand'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;">auto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|:100-1'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--reverse'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--complement'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;">noto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|:1-100'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">auto_strand</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">noto_strand</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">filecmp</span><span class="p">.</span><span class="nb" style="color: #0086b3;">cmp</span><span class="p">(</span><span class="n" style="color: #333;">auto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">noto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_regexp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not_regexp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR'</span><span class="p">,</span><span class="s" style="color: #d14;">'-v'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not_regexp_multi</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-v'</span><span class="p">])</span></span></pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">BedError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_short_line_lengths</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bed'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/malformed.bed'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_file</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_split_entry</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--split-files'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">])</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">'gi557361099gbKF435150.1.fasta'</span><span class="p">)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'gi557361099gbKF435150.1.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_error</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|:1-1000'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_warning</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'foo'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_auto_strand</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">""" Test that --auto-strand produces the same output as --reverse --complement"""</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">auto_strand</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">noto_strand</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--auto-strand'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;">auto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|:100-1'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--reverse'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--complement'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;">noto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|:1-100'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">auto_strand</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">noto_strand</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">filecmp</span><span class="p">.</span><span class="nb" style="color: #0086b3;">cmp</span><span class="p">(</span><span class="n" style="color: #333;">auto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">noto_strand</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_regexp</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not_regexp</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR'</span><span class="p">,</span><span class="s" style="color: #d14;">'-v'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_not_regexp_multi</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-v'</span><span class="p">])</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#a222b1e8057a77c62c76a9361c638233eacbd151"><strong>tests/test_feature_bounds_check.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Faidx</span><span class="p">,</span> <span class="n" style="color: #333;">Fasta</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureZeroLength</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="s" style="color: #d14;">"""Tests for handling zero-length entries, added in #155"""</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">""">A</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_zero</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">""">A</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">ATCG</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">>B</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">>C</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,185 +16,172 @@ ATCG</td>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">>D</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">GTA</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;">GC"""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_index_zero_length</span><span class="p">(</span><span class="bp" style="color: #999;">se<span class="idiff right">lf</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="idiff left right"> </span> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_zero_length</span><span class="p">(</span><span class="bp" style="color: #999;">se<span class="idiff right">lf</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="idiff left right"> </span> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="idiff left right"> </span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">"B"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_index_zero_length</span><span class="p">(</span><span class="n" style="color: #333;">se<span class="idiff left right">tup_zero</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_zero_length</span><span class="p">(</span><span class="n" style="color: #333;">se<span class="idiff left right">tup_zero</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/zero_length.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">"B"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestZeroLengthSequenceSubRange</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_zero_length_subsequence</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_zero_length_subsequence</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureBoundsCheck</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_entry</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'ATGACATCATTTTCCACCTCTGCTCAGTGTTCAACATCTGA'</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">'CAGTGCTTGCAGGATCTCTCCTGGACAAATCAATCAGGTACGACCA'</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">'AAACTGCCGCTTTTGAAGATTTTGCATGCAGCAGGTGCGCAAGG'</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">'TGAAATGTTCACTGTTAAAGAGGTCATGCACTATTTAGGTCAGTACAT'</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">'AATGGTGAAGCAACTTTATGATCAGCAGGAGCAGCATATGGTATATTG'</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">'TGGTGGAGATCTTTTGGGAGAACTACTGGGACGTCAGAGCTTCTCCGTG'</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">'AAAGACCCAAGCCCTCTCTATGATATGCTAAGAAAGAATCTTGTCACTTT'</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">'AGCCACTGCTACTACAGCAAAGTGCAGAGGAAAGTTCCACTTCCAGAAAAA'</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">'GAACTACAGAAGACGATATCCCCACACTGCCTACCTCAGAGCATAAATGCA'</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">'TACATTCTAGAGAAGGTGATTGAAGTGGGAAAAAATGATGACCTGGAGGACTC'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_middle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_end</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rev</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GA'</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_past_bounds</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">5000</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_negative</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_reversed_coordinates</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_keyerror</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch a key that does not exist """</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|joe|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_blank_string</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">""" seq[0:0] should return a blank string mdshw5/pyfaidx#53 """</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_beginning</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ATGA'</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_end</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">:]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACTC'</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_start</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_consistency</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_faidx</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_fasta</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">))</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">101</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_negate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">101</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false_negate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span></pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_zero_length_subsequence</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_zero_length_subsequence</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">100</span><span class="p">]</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_whole_entry</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'ATGACATCATTTTCCACCTCTGCTCAGTGTTCAACATCTGA'</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'CAGTGCTTGCAGGATCTCTCCTGGACAAATCAATCAGGTACGACCA'</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">'AAACTGCCGCTTTTGAAGATTTTGCATGCAGCAGGTGCGCAAGG'</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">'TGAAATGTTCACTGTTAAAGAGGTCATGCACTATTTAGGTCAGTACAT'</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="s" style="color: #d14;">'AATGGTGAAGCAACTTTATGATCAGCAGGAGCAGCATATGGTATATTG'</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">'TGGTGGAGATCTTTTGGGAGAACTACTGGGACGTCAGAGCTTCTCCGTG'</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">'AAAGACCCAAGCCCTCTCTATGATATGCTAAGAAAGAATCTTGTCACTTT'</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">'AGCCACTGCTACTACAGCAAAGTGCAGAGGAAAGTTCCACTTCCAGAAAAA'</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">'GAACTACAGAAGACGATATCCCCACACTGCCTACCTCAGAGCATAAATGCA'</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">'TACATTCTAGAGAAGGTGATTGAAGTGGGAAAAAATGATGACCTGGAGGACTC'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_middle</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_end</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TC'</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rev</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GA'</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">481</span><span class="p">)</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span><span class="p">,</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_past_bounds</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">5000</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_negative</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_reversed_coordinates</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch starting with a negative coordinate """</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_keyerror</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch a key that does not exist """</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|joe|gb|KF435150.1|'</span><span class="p">,</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_blank_string</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">""" seq[0:0] should return a blank string mdshw5/pyfaidx#53 """</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_beginning</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ATGA'</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_from_end</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">:]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACTC'</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_start</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_consistency</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">])</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_faidx</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">).</span><span class="n" style="color: #333;">end</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_74_end_fasta</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">f0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f0</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f1</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">90</span><span class="p">].</span><span class="n" style="color: #333;">end</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">end0</span><span class="p">,</span> <span class="n" style="color: #333;">end1</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">end0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">end1</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">101</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_negate</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">101</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">105</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_79_fix_one_based_false_negate</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">one_based_attributes</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="p">:</span><span class="mi" style="color: #099;">105</span><span class="p">]</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="mi" style="color: #099;">105</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#6f714b56ba3f46a151ee2b91022a458fd9c8e6e5"><strong>tests/test_feature_default_seq.py</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Faidx</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureDefaultSeq</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border_padded</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">default_seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TCNNNNNNNNNNNNNNNNNNN'</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span></pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fetch_border_padded</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch past the end of a gene entry """</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">default_seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TCNNNNNNNNNNNNNNNNNNN'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="mi" style="color: #099;">480</span><span class="p">,</span> <span class="mi" style="color: #099;">500</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#0d3f0a3598baee5caaf42b338be8317f0edf4902"><strong>tests/test_feature_indexing.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">getmtime</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Faidx</span><span class="p">,</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">,</span> <span class="n" style="color: #333;">IndexNotFoundError</span><span class="p">,</span> <span class="n" style="color: #333;">FastaNotFoundError</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.plugins.skip</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Skip</span><span class="p">,</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">,</span> <span class="n" style="color: #333;">mkdtemp</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,333 +17,336 @@ import six.moves.builtins as builtins</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestIndexing</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1| 3510 114 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1| 481 3789 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1| 642 4368 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1| 4573 5141 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215.1| 5317 9901 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212.1| 5374 15415 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507.1| 2848 60824 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081.1| 1009 63849 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080.1| 4884 65009 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1| 2819 70099 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_141</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1| 3510 115 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1| 481 3842 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1| 642 4429 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1| 4573 5213 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215.1| 5317 10040 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1| 2819 71079 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_141.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_141.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1| 3510 114 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1| 481 3789 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1| 642 4368 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1| 4573 5141 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215.1| 5317 9901 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212.1| 5374 15415 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583788|ref|NM_001282545.1| 4170 20980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583786|ref|NM_001282543.1| 5466 25324 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583785|ref|NM_000465.3| 5523 30980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583740|ref|NM_001282549.1| 3984 36696 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583738|ref|NM_001282548.1| 4113 40851 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384540|ref|XM_005249645.1| 2752 45151 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384538|ref|XM_005249644.1| 3004 48071 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384536|ref|XM_005249643.1| 3109 51246 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384534|ref|XM_005249642.1| 3097 54528 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373237|ref|XM_005265508.1| 2794 57830 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507.1| 2848 60824 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081.1| 1009 63849 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080.1| 4884 65009 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1| 2819 70099 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_111</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309 3510 114 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150 481 3789 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149 642 4368 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216 4573 5141 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215 5317 9901 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212 5374 15415 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583788|ref|NM_001282545 4170 20980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583786|ref|NM_001282543 5466 25324 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583785|ref|NM_000465 5523 30980 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583740|ref|NM_001282549 3984 36696 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583738|ref|NM_001282548 4113 40851 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384540|ref|XM_005249645 2752 45151 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373237|ref|XM_005265508 2794 57830 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507 2848 60824 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081 1009 63849 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080 4884 65009 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079 2819 70099 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">read_long_names</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">_index_as_string</span><span class="p">())</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_141</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1| 3510 115 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1| 481 3842 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1| 642 4429 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1| 4573 5213 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215.1| 5317 10040 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212.1| 5374 15631 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081.1| 1009 64742 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080.1| 4884 65918 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1| 2819 71079 70 72</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_141.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_141.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_order</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583788|ref|NM_001282545.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583786|ref|NM_001282543.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583785|ref|NM_000465.3|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583740|ref|NM_001282549.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583738|ref|NM_001282548.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384540|ref|XM_005249645.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384538|ref|XM_005249644.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384536|ref|XM_005249643.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384534|ref|XM_005249642.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373237|ref|XM_005265508.1|"</span><span class="p">,</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507.1|"</span><span class="p">,</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081.1|"</span><span class="p">,</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080.1|"</span><span class="p">,</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1|"</span><span class="p">)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">order</span></span>
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84
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_111</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309 3510 114 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583738|ref|NM_001282548 4113 40851 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384540|ref|XM_005249645 2752 45151 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384538|ref|XM_005249644 3004 48071 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384536|ref|XM_005249643 3109 51246 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384534|ref|XM_005249642 3097 54528 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373237|ref|XM_005265508 2794 57830 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507 2848 60824 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081 1009 63849 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080 4884 65009 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079 2819 70099 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">read_long_names</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">_index_as_string</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_order</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"gi|563317589|dbj|AB821309.1|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gi|557361099|gb|KF435150.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|557361097|gb|KF435149.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583796|ref|NR_104216.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583795|ref|NR_104215.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583794|ref|NR_104212.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583788|ref|NM_001282545.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583786|ref|NM_001282543.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583785|ref|NM_000465.3|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583740|ref|NM_001282549.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|543583738|ref|NM_001282548.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384540|ref|XM_005249645.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384538|ref|XM_005249644.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384536|ref|XM_005249643.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530384534|ref|XM_005249642.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373237|ref|XM_005265508.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530373235|ref|XM_005265507.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364726|ref|XR_241081.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364725|ref|XR_241080.1|"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="s" style="color: #d14;">"gi|530364724|ref|XR_241079.1|"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">order</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_valgrind_short_lines</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="s" style="color: #d14;">""" Makes all full-length lines short and checks that error is raised</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="s" style="color: #d14;"> in all appropriate circumstances.</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/23212515/717419</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Windows'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">n_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_lines</span><span class="p">):</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">71</span><span class="p">:</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">:</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">full_line</span><span class="p">:</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">indexed</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_valgrind_long_lines</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="s" style="color: #d14;">""" Makes all full-length lines long and checks that error is raised</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> in all appropriate circumstances.</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/23212515/717419</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Windows'</span><span class="p">:</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">n_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_lines</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">71</span><span class="p">:</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'NNN'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">:</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">full_line</span><span class="p">:</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">indexed</span><span class="p">)</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_valgrind_short_lines</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="s" style="color: #d14;">""" Makes all full-length lines short and checks that error is raised</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> in all appropriate circumstances.</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/23212515/717419</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Windows'</span><span class="p">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">n_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_lines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">71</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">full_line</span><span class="p">:</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">indexed</span><span class="p">)</span></span>
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195
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_valgrind_<span class="idiff">blank</span>_lines</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"><span class="idiff left"> </span> <span class="s" style="color: #d14;">""" Makes all full-length lines <span class="idiff right">blank</span> and checks that error is raised</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span> in all appropriate circumstances.</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span> """</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/23212515/717419</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Windows'</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"><span class="idiff left right"> </span> <span class="n" style="color: #333;">indexed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"><span class="idiff left right"> </span> <span class="n" style="color: #333;">n_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_lines</span><span class="p">):</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">71</span><span class="p">:</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">:</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">full_line</span><span class="p">:</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">indexed</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_valgrind_<span class="idiff left">long</span>_lines</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff right">remove_index</span></span><span class="p">):</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="s" style="color: #d14;">""" Makes all full-length lines <span class="idiff left right">long</span> and checks that error is raised</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> in all appropriate circumstances.</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/23212515/717419</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Windows'</span><span class="p">:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">n_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_lines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">71</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'NNN'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">full_line</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">indexed</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reindex_on_modification</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">""" This test ensures that the index is regenerated when the FASTA</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"><span class="s" style="color: #d14;"> modification time is newer than the index modification time.</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"><span class="s" style="color: #d14;"> mdshw5/pyfaidx#50 """</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">index_mtime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getmtime</span><span class="p">(</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">indexname</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">index_mtime</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">getmtime</span><span class="p">(</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">indexname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">index_mtime</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_valgrind_blank_lines</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="s" style="color: #d14;">""" Makes all full-length lines blank and checks that error is raised</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;"> in all appropriate circumstances.</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/23212515/717419</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Windows'</span><span class="p">:</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">SkipTest</span></span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">n_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_lines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">71</span><span class="p">:</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">full_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">full_line</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">indexed</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">indexed</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_83</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that blank lines between entries are treated in the</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"><span class="s" style="color: #d14;"> same way as samtools 1.2. See mdshw5/pyfaidx#83.</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"MT 119 4 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">GL000207.1 60 187 60 61</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_83.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_83.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reindex_on_modification</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="s" style="color: #d14;">""" This test ensures that the index is regenerated when the FASTA</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"><span class="s" style="color: #d14;"> modification time is newer than the index modification time.</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"><span class="s" style="color: #d14;"> mdshw5/pyfaidx#50 """</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">index_mtime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getmtime</span><span class="p">(</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">indexname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">utime</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">index_mtime</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">getmtime</span><span class="p">(</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">indexname</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">index_mtime</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_96_fail_build_faidx</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that the fasta file is closed if construction of the 'Faidx' file</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;"> when attempting to build an index.</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"><span class="s" style="color: #d14;"> See mdshw5/pyfaidx#96</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_96.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write simple fasta file with inconsistent sequence line lengths,</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># so building an index raises a 'FastaIndexingError'</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_out</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="s" style="color: #d14;">">seq1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">CTCCGGGCCCAT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">AACACTTGGGGGTAGCTAAAGTGAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ATAAAGCCTAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_83</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that blank lines between entries are treated in the</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;"> same way as samtools 1.2. See mdshw5/pyfaidx#83.</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">expect_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"MT 119 4 70 71</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">GL000207.1 60 187 60 61</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_83.fasta'</span><span class="p">).</span><span class="n" style="color: #333;">indexname</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/issue_83.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect_index</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">builtins_open</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">builtins</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_96_fail_build_faidx</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that the fasta file is closed if construction of the 'Faidx' file</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"><span class="s" style="color: #d14;"> when attempting to build an index.</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;"> See mdshw5/pyfaidx#96</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_96.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write simple fasta file with inconsistent sequence line lengths,</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># so building an index raises a 'FastaIndexingError'</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_out</span><span class="p">:</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="s" style="color: #d14;">">seq1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">CTCCGGGCCCAT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">AACACTTGGGGGTAGCTAAAGTGAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ATAAAGCCTAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">opened_files</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[]</span></span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">builtins_open</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">builtins</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">open</span></span></span>
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266
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">builtins_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">opened_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">opened_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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271
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">mock</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">'six.moves.builtins.open'</span><span class="p">,</span> <span class="n" style="color: #333;">side_effect</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">test_open</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertFail</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="s" style="color: #d14;">"Faidx construction should fail with 'FastaIndexingError'."</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">closed</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">opened_files</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">builtins_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">opened_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_96_fail_read_malformed_index_duplicate_key</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that the fasta file is closed if construction of the 'Faidx' file</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;"> fails when attempting to read a pre-existing index. The index is malformed because</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"><span class="s" style="color: #d14;"> it contains mulitple occurrences of the same index.</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;"> See mdshw5/pyfaidx#96</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_96.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">faidx_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_96.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write simple fasta file</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_out</span><span class="p">:</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">seq1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">CTCCGGGCCCAT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ATAAAGCCTAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">faidx_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">faidx_out</span><span class="p">:</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">faidx_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"seq1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">13</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">seq1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">13</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">mock</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">'six.moves.builtins.open'</span><span class="p">,</span> <span class="n" style="color: #333;">side_effect</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">test_open</span><span class="p">):</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">remove_index</span><span class="p">.</span><span class="n" style="color: #333;">assertFail</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="s" style="color: #d14;">"Faidx construction should fail with 'FastaIndexingError'."</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">FastaIndexingError</span><span class="p">:</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">closed</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">opened_files</span><span class="p">)</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">builtins_open</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">builtins</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_build_issue_96_fail_read_malformed_index_duplicate_key</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that the fasta file is closed if construction of the 'Faidx' file</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> fails when attempting to read a pre-existing index. The index is malformed because</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> it contains mulitple occurrences of the same index.</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> See mdshw5/pyfaidx#96</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_96.fasta'</span><span class="p">)</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">faidx_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_96.fasta.fai'</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write simple fasta file</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_out</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">seq1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">CTCCGGGCCCAT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ATAAAGCCTAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">faidx_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">faidx_out</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">faidx_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"seq1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">13</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">seq1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">24</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">12</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">13</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">opened_files</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[]</span></span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">builtins_open</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">builtins</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">open</span></span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">builtins_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">opened_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">opened_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">mock</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">'six.moves.builtins.open'</span><span class="p">,</span> <span class="n" style="color: #333;">side_effect</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">test_open</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertFail</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="s" style="color: #d14;">"Faidx construction should fail with 'ValueError'."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">closed</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">opened_files</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">builtins_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">opened_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_back_index</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure that index files written with write_fai() can be read back"""</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">locale</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">old_locale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">getlocale</span><span class="p">(</span><span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">LC_NUMERIC</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">setlocale</span><span class="p">(</span><span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">LC_NUMERIC</span><span class="p">,</span> <span class="s" style="color: #d14;">'en_US.utf8'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">write_fai</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">build_index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">setlocale</span><span class="p">(</span><span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">LC_NUMERIC</span><span class="p">,</span> <span class="n" style="color: #333;">old_locale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">mock</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">'six.moves.builtins.open'</span><span class="p">,</span> <span class="n" style="color: #333;">side_effect</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">test_open</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">)</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">remove_index</span><span class="p">.</span><span class="n" style="color: #333;">assertFail</span><span class="p">(</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="s" style="color: #d14;">"Faidx construction should fail with 'ValueError'."</span><span class="p">)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">closed</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">opened_files</span><span class="p">)</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">IndexNotFoundError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_134_no_build_index</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that index file is not built when build_index=False. See mdshw5/pyfaidx#134.</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_back_index</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure that index files written with write_fai() can be read back"""</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">locale</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> </span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Linux"</span><span class="p">:</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">new_locale</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'en_US.utf8'</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Darwin"</span><span class="p">:</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">new_locale</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'en_US.UTF-8'</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">old_locale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">getlocale</span><span class="p">(</span><span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">LC_NUMERIC</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">setlocale</span><span class="p">(</span><span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">LC_NUMERIC</span><span class="p">,</span> <span class="n" style="color: #333;">new_locale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">write_fai</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">build_index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">setlocale</span><span class="p">(</span><span class="n" style="color: #333;">locale</span><span class="p">.</span><span class="n" style="color: #333;">LC_NUMERIC</span><span class="p">,</span> <span class="n" style="color: #333;">old_locale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">IndexNotFoundError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_134_no_build_index</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that index file is not built when build_index=False. See mdshw5/pyfaidx#134.</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">build_index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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337
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FastaIndexingError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_144_no_defline</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that an exception is raised when a file contains no deflines. See mdshw5/pyfaidx#144.</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_144.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write simple fasta file</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_out</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"CTCCGGGCCCAT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ATAAAGCCTAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> </span></pre>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FastaIndexingError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_144_no_defline</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="s" style="color: #d14;">""" Ensure that an exception is raised when a file contains no deflines. See mdshw5/pyfaidx#144.</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkdtemp</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">fasta_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'issue_144.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write simple fasta file</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_out</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"CTCCGGGCCCAT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ATAAAGCCTAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="n" style="color: #333;">fasta_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#64ec433b3b32854e3f3ada287ab6ea004569952d"><strong>tests/test_feature_key_function.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Faidx</span><span class="p">,</span> <span class="n" style="color: #333;">Fasta</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,49 +31,47 @@ def get_duplicated_gene_name(accession):</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ACCESSION_TO_DUPLICATED_GENE_NAME_DICT</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">accession</span><span class="p">,</span> <span class="n" style="color: #333;">accession</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureKeyFunction</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">genes</span> <span class="c1" style="color: #998; font-style: italic;"># Support feature introduced in #111</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">genes</span> <span class="c1" style="color: #998; font-style: italic;"># Support feature introduced in #111</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">te<span class="idiff">arDown</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">try</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">remove</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'data/genes.fasta.fai'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">except</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">EnvironmentError</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">pass</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># some tests may delete this file</span></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">te<span class="idiff left">st_keys</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">remove_index</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">genes</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Fasta</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'data/genes.fasta'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key_function</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">get_gene_name</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">expect</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'BARD1'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'FGFR2'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'MDM4'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530364724|ref|XR_241079.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530364725|ref|XR_241080.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530364726|ref|XR_241081.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530373235|ref|XM_005265507.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530373237|ref|XM_005265508.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384534|ref|XM_005249642.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384536|ref|XM_005249643.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384538|ref|XM_005249644.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384540|ref|XM_005249645.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583738|ref|NM_001282548.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583740|ref|NM_001282549.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583785|ref|NM_000465.3|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583786|ref|NM_001282543.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583788|ref|NM_001282545.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583794|ref|NR_104212.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583795|ref|NR_104215.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|557361097|gb|KF435149.1|'</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">result</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">genes</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">())</span></span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">assert</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">expect</span></span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key<span class="idiff">s</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"><span class="idiff left right"> </span> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_gene_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="idiff left"> </span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'BARD1'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'FGFR2'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'MDM4'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530364724|ref|XR_241079.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530364725|ref|XR_241080.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530364726|ref|XR_241081.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530373235|ref|XM_005265507.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530373237|ref|XM_005265508.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384534|ref|XM_005249642.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384536|ref|XM_005249643.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384538|ref|XM_005249644.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|530384540|ref|XM_005249645.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583738|ref|NM_001282548.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583740|ref|NM_001282549.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583785|ref|NM_000465.3|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583786|ref|NM_001282543.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583788|ref|NM_001282545.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583794|ref|NR_104212.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|543583795|ref|NR_104215.1|'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gi|557361097|gb|KF435149.1|'</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="idiff left"> </span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">genes</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">())</span></span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key<span class="idiff left">_function_by_dictionary_get_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">remove_index</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_gene_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">genes</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'MDM4'</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:</span></span><span class="mi" style="color: #099;"><span class="idiff">150</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">result</span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_function_by_dictionary_get_key</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_gene_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="s" style="color: #d14;">'MDM4'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_function_by_fetch</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_gene_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'MDM4'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_function_by_fetch</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_gene_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'MDM4'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_duplicated_keys</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_duplicated_gene_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_duplicated_keys</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_duplicated_gene_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_duplicated_keys_shortest</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_duplicated_gene_name</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"shortest"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4573</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="s" style="color: #d14;">"BARD1"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_duplicated_keys_shortest</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_duplicated_gene_name</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"shortest"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4573</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="s" style="color: #d14;">"BARD1"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_duplicated_keys_longest</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_duplicated_gene_name</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"longest"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5317</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="s" style="color: #d14;">"BARD1"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span></pre>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_duplicated_keys_longest</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">key_function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_duplicated_gene_name</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"longest"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5317</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="s" style="color: #d14;">"BARD1"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">result</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#562f427754839d2bd05384aefeb4ddf62625a252"><strong>tests/test_feature_read_ahead_buffer.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Faidx</span><span class="p">,</span> <span class="n" style="color: #333;">Fasta</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureBuffer</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_false</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_true</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_exceed</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'atgacatcattttccacctctgctcagtgttcaacatctgacagtgcttgcaggatctctcctggacaaatcaatcaggtacgaccaaaactgccgcttttgaagattttgcatgcagcaggtgcgcaaggtgaaatgttcactgttaaagaggtcatgcactatttaggtcagtacataatggtgaagcaactttatgatcagcaggagcagcatatggtatattgtggtggagatcttttgggagaactactgggacgtcagagcttctccgtgaaagacccaagccctctctatgatatgctaagaaagaatcttgtcactttagccactgctactacagcaaagtgcagaggaaagttccacttccagaaaaagaactacagaagacgatatcccc'</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">400</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_bounds_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">15000</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_false</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_true</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_exceed</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'atgacatcattttccacctctgctcagtgttcaacatctgacagtgcttgcaggatctctcctggacaaatcaatcaggtacgaccaaaactgccgcttttgaagattttgcatgcagcaggtgcgcaaggtgaaatgttcactgttaaagaggtcatgcactatttaggtcagtacataatggtgaagcaactttatgatcagcaggagcagcatatggtatattgtggtggagatcttttgggagaactactgggacgtcagagcttctccgtgaaagacccaagccctctctatgatatgctaagaaagaatcttgtcactttagccactgctactacagcaaagtgcagaggaaagttccacttccagaaaaagaactacagaagacgatatcccc'</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">400</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">FetchError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_bounds_error</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">strict_bounds</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">15000</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_buffer_value</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">read_ahead</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Faidx</span><span class="p">,</span> <span class="n" style="color: #333;">Fasta</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureSequenceAsRaw</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_false</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_true</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_false_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_true_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_type_when_blen_lt_0</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span></pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_false</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_true</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_false_error</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_true_error</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_as_raw_type_when_blen_lt_0</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">as_raw</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#4c32d79098dfd4a5964f9258d84c3e5152b387b2"><strong>tests/test_feature_spliced_seq.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Fasta</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureSplicedSeq</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">fais</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">"data/gene.bed12.fasta.fai"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">"data/chr17.hg19.part.fa.fai"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fai</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fais</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">fai</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_split_seq</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch sequence by blocks """</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr17.hg19.part.fa'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">"data/gene.bed12.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]][:].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/gene.bed12"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">bed</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fi</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fi</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">fais</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">"data/gene.bed12.fasta.fai"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">"data/chr17.hg19.part.fa.fai"</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fai</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fais</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">fai</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_split_seq</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">""" Fetch sequence by blocks """</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr17.hg19.part.fa'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">"data/gene.bed12.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span><span class="p">[</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]][:].</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"data/gene.bed12"</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">bed</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fi</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fi</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parse bed12 format</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">starts</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">size</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">sizes</span><span class="p">)]</span> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># bed half-open</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">starts</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ends</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">get_spliced_seq</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">intervals</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"===="</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parse bed12 format</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">starts</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">size</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">sizes</span><span class="p">)]</span> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># bed half-open</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">starts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">starts</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ends</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">get_spliced_seq</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">intervals</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"===="</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_seq_rc</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">""" Check get_seq with rc argument """</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr17.hg19.part.fa'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">get_seq</span><span class="p">(</span><span class="s" style="color: #d14;">"chr17"</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CCCTGTTCCT"</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"normal"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">get_seq</span><span class="p">(</span><span class="s" style="color: #d14;">"chr17"</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"AGGAACAGGG"</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"rc"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_get_seq_rc</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="s" style="color: #d14;">""" Check get_seq with rc argument """</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/chr17.hg19.part.fa'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">get_seq</span><span class="p">(</span><span class="s" style="color: #d14;">"chr17"</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CCCTGTTCCT"</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"normal"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fa</span><span class="p">.</span><span class="n" style="color: #333;">get_seq</span><span class="p">(</span><span class="s" style="color: #d14;">"chr17"</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"AGGAACAGGG"</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"rc"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">expect</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#7eaf1cf32558b6c04e3d6d91f5123a1cf5adfa59"><strong>tests/test_feature_split_char.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Faidx</span><span class="p">,</span> <span class="n" style="color: #333;">Fasta</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFeatureSplitChar</span><span class="p">(</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tearDown</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_keys</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"drop"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'530364724'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530364725'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530364726'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530373235'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530373237'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384534'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384536'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384538'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384540'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583738'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583740'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583785'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583786'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583788'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583794'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583795'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583796'</span><span class="p">,</span> <span class="s" style="color: #d14;">'557361097'</span><span class="p">,</span> <span class="s" style="color: #d14;">'557361099'</span><span class="p">,</span> <span class="s" style="color: #d14;">'563317589'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AB821309.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'KF435149.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'KF435150.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_000465.3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282543.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282545.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282548.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282549.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NR_104212.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NR_104215.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NR_104216.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249642.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249643.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249644.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249645.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005265507.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005265508.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR_241079.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR_241080.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR_241081.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'dbj'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_function_by_dictionary_get_key</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"drop"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'KF435150.1'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_function_by_fetch</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"drop"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'KF435150.1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_stop</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_index</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta.fai'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">EnvironmentError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># some tests may delete this file</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_keys</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"drop"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'530364724'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530364725'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530364726'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530373235'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530373237'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384534'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384536'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384538'</span><span class="p">,</span> <span class="s" style="color: #d14;">'530384540'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583738'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583740'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583785'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583786'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583788'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583794'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583795'</span><span class="p">,</span> <span class="s" style="color: #d14;">'543583796'</span><span class="p">,</span> <span class="s" style="color: #d14;">'557361097'</span><span class="p">,</span> <span class="s" style="color: #d14;">'557361099'</span><span class="p">,</span> <span class="s" style="color: #d14;">'563317589'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AB821309.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'KF435149.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'KF435150.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_000465.3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282543.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282545.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282548.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NM_001282549.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NR_104212.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NR_104215.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NR_104216.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249642.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249643.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249644.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005249645.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005265507.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XM_005265508.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR_241079.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR_241080.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XR_241081.1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'dbj'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_function_by_dictionary_get_key</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"drop"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">[</span><span class="s" style="color: #d14;">'KF435150.1'</span><span class="p">][</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">150</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_key_function_by_fetch</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">faidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faidx</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">,</span> <span class="n" style="color: #333;">duplicate_action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"drop"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="s" style="color: #d14;">'KF435150.1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expect</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_stop</span><span class="p">(</span><span class="n" style="color: #333;">remove_index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Fasta</span><span class="p">(</span><span class="s" style="color: #d14;">'data/genes.fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">split_char</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'|'</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/dc77492add9a5b16255c9777414cb64fa0937280#918f1a692b59c81cf124edb2f54a5d18717f080e"><strong>tests/test_sequence_class.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyfaidx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">complement</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">assert_raises</span><span class="p">,</span> <span class="n" style="color: #333;">raises</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">,</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">150</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,8 +19,9 @@ def test_negate_metadata():</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">seq_neg</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">seq_neg</span><span class="p">.</span><span class="n" style="color: #333;">__repr__</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">[::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">__repr__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">xfail</span><span class="p">(</span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_seq_invalid</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">assert_raises</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">ValueError</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">seq_invalid</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">seq_invalid</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p"><span class="idiff left right">(</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_integer_index</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'T'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,11 +29,11 @@ def test_integer_index():</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_slice_index</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">10</span><span class="p">].</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'TTGAAGATTT'</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p"><span class="idiff left right">(</span></span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mark</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xfail</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_comp_invalid</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">complement</span><span class="p">(</span><span class="n" style="color: #333;">comp_invalid</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">raises</span><span class="p"><span class="idiff left right">(</span></span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;"><span class="idiff left">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mark</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">xfail</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">raises</span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_check_coordinates</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gi|557361099|gb|KF435150.1|'</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">110</span><span class="p">)</span></span>
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