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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pyfaidx">Debian Med / python-pyfaidx</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb">739f7379</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-01-01T19:58:11+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.5.7</pre>
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<h4>7 changed files:</h4>
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#83b1dda3455005121b48aadc1fefedc1b5e999ea">
pyfaidx/__init__.py
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<li class="file-stats">
<a href="#acca83fee2a805bc9377545bfbdbd21c69d727ac">
pyfaidx/cli.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.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="#a222b1e8057a77c62c76a9361c638233eacbd151">
tests/test_feature_bounds_check.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -7,9 +7,7 @@ python:</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.6'</span></span>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
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<td class="diff-line-num new_line" data-linenumber="8" 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.5'</span></span>
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<td class="diff-line-num new_line" data-linenumber="9" 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.4'</span></span>
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<td class="diff-line-num new_line old" data-linenumber="10" 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="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.3'</span></span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
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<td class="diff-line-num new_line" data-linenumber="10" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">2.7'</span></span>
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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">2.6'</span></span>
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<td class="diff-line-num new_line" data-linenumber="11" 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">pypy'</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">pypy3'</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<li id="561b88e19de321ca62c7590bbb350765fb110905">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">|Travis| |PyPI| |<span class="idiff left right">Landscape| |Coverage| |Depsy| |Appveyor</span>|</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">|Travis| |PyPI| |<span class="idiff left right">Coverage| |Depsy</span>|</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Description</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">-----------</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="54" 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">@@ -54,7 +54,8 @@ Acts like a dictionary.</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">.. code:: python</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> >>> genes.keys() ('AB821309.1', 'KF435150.1', 'KF435149.1', 'NR_104216.1', 'NR_104215.1', 'NR_104212.1', 'NM_001282545.1', 'NM_001282543.1', 'NM_000465.3', 'NM_001282549.1', 'NM_001282548.1', 'XM_005249645.1', 'XM_005249644.1', 'XM_005249643.1', 'XM_005249642.1', 'XM_005265508.1', 'XM_005265507.1', 'XR_241081.1', 'XR_241080.1', 'XR_241079.1')</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> >>> genes.keys()</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> ('AB821309.1', 'KF435150.1', 'KF435149.1', 'NR_104216.1', 'NR_104215.1', 'NR_104212.1', 'NM_001282545.1', 'NM_001282543.1', 'NM_000465.3', 'NM_001282549.1', 'NM_001282548.1', 'XM_005249645.1', 'XM_005249644.1', 'XM_005249643.1', 'XM_005249642.1', 'XM_005265508.1', 'XM_005265507.1', 'XR_241081.1', 'XR_241080.1', 'XR_241079.1')</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> >>> genes['NM_001282543.1'][200:230]</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> >NM_001282543.1:201-230</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">@@ -544,7 +545,7 @@ Support for compressed FASTA</td>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="plaintext">----------------------------</span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="plaintext">``pyfaidx`` can create and read ``.fai`` indices for FASTA files that have</span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="plaintext">been compressed using the `bgzip <http<span class="idiff left right">://www.htslib.org/doc/tabix</span>.html>`_</span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext">been compressed using the `bgzip <http<span class="idiff left right">s://www.htslib.org/doc/bgzip</span>.html>`_</span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="plaintext">tool from `samtools <http://www.htslib.org/>`_. ``bgzip`` writes compressed</span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="plaintext">data in a ``BGZF`` format. ``BGZF`` is ``gzip`` compatible, consisting of</span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="plaintext">multiple concatenated ``gzip`` blocks, each with an additional ``gzip``</span>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb#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">@@ -25,7 +25,7 @@ if sys.version_info > (3, ):</td>
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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="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="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)'</span><span class="p">)</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;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.5.<span class="idiff left right">5.2</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC28" 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;">'0.5.<span class="idiff left right">7</span>'</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>
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<pre style="margin: 0;"> <span id="LC31" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,7 +123,7 @@ class Sequence(object):</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> >chr1</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> AC</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</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="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</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="mi" style="color: #099;"><span class="idiff right">0</span></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;">correction_factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</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">@@ -461,7 +461,7 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="n" style="color: #333;">rlen</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">lenc</span><span class="p">,</span> <span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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="LC462" class="line" lang="python"> <span class="n" style="color: #333;">rlen</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">lenc</span><span class="p">,</span> <span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">rlen</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">lenc</span><span class="p">,</span> <span class="n" style="color: #333;">lenb</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"> <span class="n" style="color: #333;">newlines</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;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">lenc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lenc</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"> <span class="n" style="color: #333;">newlines</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;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">lenc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lenc</span><span class="p">))</span><span class="idiff left"> </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">lenc</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">bend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newlines</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rlen</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IndexRecord</span><span class="p">(</span><span class="n" style="color: #333;">rlen</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">lenc</span><span class="p">,</span> <span class="n" style="color: #333;">lenb</span><span class="p">,</span> <span class="n" style="color: #333;">bend</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">prev_bend</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">@@ -508,8 +508,8 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># reference sequence name</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># binary offset of end of current line</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># reference character length</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span> <span class="c1" style="color: #998; font-style: italic;"># binary line length (includes newline)</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"> <span class="n" style="color: #333;">clen</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span> <span class="c1" style="color: #998; font-style: italic;"># character line length</span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span> <span class="c1" style="color: #998; font-style: italic;"># binary line length (includes newline)</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="n" style="color: #333;">clen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span> <span class="c1" style="color: #998; font-style: italic;"># character line length</span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">bad_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># lines > || < than blen</span></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">thisoffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">valid_entry</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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">@@ -535,9 +535,9 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python"> <span class="s" style="color: #d14;">"Inconsistent line found in >{0} at "</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"> <span class="s" style="color: #d14;">"line {1:n}."</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="n" style="color: #333;">bad_lines</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="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">clen</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">clen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">bad_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># must catch empty deflines (actually these might be okay: https://github.com/samtools/htslib/pull/258)</span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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\r</span><span class="s" style="color: #d14;">'</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="n" style="color: #333;">split</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">@@ -648,8 +648,8 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Calculate offset (https://github.com/samtools/htslib/blob/20238f354894775ed22156cdd077bc0d544fa933/faidx.c#L398)</span></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"> <span class="n" style="color: #333;">newlines_before</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">start0</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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span><span class="p">))</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">newlines_to_end</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;">end</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">start0</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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span><span class="p">))</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lenc</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">newlines_to_end</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;">end</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span><span class="p">))</span><span class="idiff left"> </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">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lenc</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="python"> <span class="n" style="color: #333;">newlines_inside</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newlines_to_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newlines_before</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python"> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newlines_inside</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_len</span></span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="python"> <span class="n" style="color: #333;">bstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newlines_before</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start0</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">@@ -669,12 +669,15 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC669" 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="LC670" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">bstart</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the requested sequence exceeds len(FastaRecord), return as much as possible</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bstart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bend</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strict_bounds</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bstart</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Otherwise it should be safe to read the sequence</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">seq_blen</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strict_bounds</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the requested sequence is negative, we will pad the empty string with default_seq.</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This was changed to support #155 with strict_bounds=True.</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"> <span class="n" style="color: #333;">seq</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="LC682" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC683" 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;">internals</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">@@ -994,13 +997,9 @@ class Fasta(object):</td>
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<pre style="margin: 0;"> <span id="LC997" class="line" lang="python"> <span class="n" style="color: #333;">sequence_always_upper</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sequence_always_upper</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="python"> <span class="n" style="color: #333;">rebuild</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rebuild</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="python"> <span class="n" style="color: #333;">build_index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">build_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span></span>
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mutable</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="python"> <span class="p">[(</span><span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="n" style="color: #333;">FastaRecord</span><span class="p">(</span><span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()])</span></span>
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mutable</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="n" style="color: #333;">MutableFastaRecord</span><span class="p">(</span><span class="n" style="color: #333;">rname</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="LC1003" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()])</span></span>
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="python"> <span class="n" style="color: #333;">_record_constructor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MutableFastaRecord</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mutable</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">FastaRecord</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">([(</span><span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="n" style="color: #333;">_record_constructor</span><span class="p">(</span><span class="n" style="color: #333;">rname</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()])</span></span>
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1004
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1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="python"></span>
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1005
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1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__contains__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">rname</span><span class="p">):</span></span>
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1006
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return True if genome contains record."""</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">@@ -1057,6 +1056,15 @@ class Fasta(object):</td>
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1057
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># len(Sequence.seq) != end - start</span></span>
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1058
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="n" style="color: #333;">name</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 class="p">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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1059
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1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="python"></span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">records</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()</span></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="python"></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">records</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="python"></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">items</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">records</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="python"></span>
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1060
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1068
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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1061
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__exit__</span><span class="p">()</span></span>
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1062
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1070
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<pre style="margin: 0;"> <span id="LC1070" 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">@@ -1258,6 +1266,21 @@ def check_bad_lines(rname, bad_lines, i):</td>
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1258
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1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unhandled exception during fasta indexing at entry "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rname</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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1259
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="python"> <span class="s" style="color: #d14;">"Please report this issue at https://github.com/mdshw5/pyfaidx/issues "</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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1260
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1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">bad_lines</span><span class="p">))</span></span>
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1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="python"> </span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_valid_filename</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">):</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="python"><span class="s" style="color: #d14;"> From https://github.com/django/django/blob/efc3e32d6d7fb9bb41be73b80c8607b653c1fbd6/django/utils/text.py#L222-L232</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="python"><span class="s" style="color: #d14;"> Return the given string converted to a string that can be used for a clean</span></span>
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1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="python"><span class="s" style="color: #d14;"> filename. Remove leading and trailing spaces; convert other spaces to</span></span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="python"><span class="s" style="color: #d14;"> underscores; and remove anything that is not an alphanumeric, dash,</span></span>
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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="python"><span class="s" style="color: #d14;"> underscore, or dot.</span></span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="python"><span class="s" style="color: #d14;"> >>> get_valid_filename("HPV16_144-1.fa")</span></span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="python"><span class="s" style="color: #d14;"> 'HPV16_144-1.fa'</span></span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="python"><span class="s" style="color: #d14;"> >>> get_valid_filename("chromosome 6.fa")</span></span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="python"><span class="s" style="color: #d14;"> 'chromosome_6.fa'</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="python"> <span class="n" style="color: #333;">s</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;">s</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">,</span> <span class="s" style="color: #d14;">'_'</span><span class="p">)</span></span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">r'(?u)[^-\w.]'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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1261
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1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="python"></span>
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1262
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="python"></span>
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1263
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1286
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<pre style="margin: 0;"> <span id="LC1286" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb#acca83fee2a805bc9377545bfbdbd21c69d727ac"><strong>pyfaidx/cli.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">@@ -3,11 +3,9 @@ import argparse</td>
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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;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>
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<pre style="margin: 0;"> <span id="LC5" 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="LC6" 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;">wrap_sequence</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span><span class="p">,</span> <span class="n" style="color: #333;">ucsc_split</span><span class="p">,</span> <span class="n" style="color: #333;">bed_split</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;">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;">wrap_sequence</span><span class="p">,</span> <span class="n" style="color: #333;">FetchError</span><span class="p">,</span> <span class="n" style="color: #333;">ucsc_split</span><span class="p">,</span> <span class="n" style="color: #333;">bed_split</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">get_valid_filename</span></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;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</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="n" style="color: #333;">keepcharacters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</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="LC10" 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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_sequence</span><span class="p">(</span><span class="n" style="color: #333;">args</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;">_</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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">@@ -36,7 +34,7 @@ def write_sequence(args):</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split_files</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># open output file based on sequence name</span></span>
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<pre style="margin: 0;"> <span id="LC36" 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;">'.'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</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="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</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;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">''</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">c</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">c</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">filename</span></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">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isalnum</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">c</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 right">keepcharacters</span></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;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">get_valid_filename</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">filename</span></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;">outfile</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;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</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;">elif</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</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;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span></span>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb#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">@@ -36,12 +36,11 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"Intended Audience :: Science/Research"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"Topic :: Scientific/Engineering :: Bio-Informatics"</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="p">]</span></span>
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<a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb#e805f7df64ccdcc7314257ec4a439be10b25e551"><strong>tests/test_FastaRecord.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">@@ -46,6 +46,7 @@ class TestFastaRecord(TestCase):</td>
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</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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<a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/739f737969497e06c16c17c0fc67c416e3524fdb#a222b1e8057a77c62c76a9361c638233eacbd151"><strong>tests/test_feature_bounds_check.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">@@ -6,6 +6,53 @@ from unittest import TestCase</td>
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</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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7
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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="o" style="font-weight: 600;">.</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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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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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;">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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11
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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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12
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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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13
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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="o" style="font-weight: 600;">.</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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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">ATCG</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">>B</span></span>
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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;">>C</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;">>D</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">GTA</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" 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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22
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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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23
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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="o" style="font-weight: 600;">.</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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24
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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="o" style="font-weight: 600;">.</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="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_index_zero_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="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>
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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_fetch_zero_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="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/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="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="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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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> </span>
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34
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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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36
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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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37
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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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39
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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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40
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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="o" style="font-weight: 600;">.</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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41
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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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42
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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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44
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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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45
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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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46
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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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47
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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="o" style="font-weight: 600;">.</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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9
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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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10
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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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11
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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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