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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pyensembl">Debian Med / pyensembl</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyensembl/-/commit/10866e8bb7190ba39b57541705eb9d8d7ce5f5e2">10866e8b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T19:55:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyensembl/-/commit/5fe011317e77c7200bbd0938248482f6da6f523c">5fe01131</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T19:55:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.9.4+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyensembl/-/commit/333f151eafed6248814e9d8626d1626ef111066e">333f151e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T19:55:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.9.4+ds'
Update to upstream version '1.9.4+ds'
with Debian dir 5eb8a7b4767adfa32a39a3e406a5ea36ca6f07a8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyensembl/-/commit/dc59c8d054b2f5c60420d2c72d00a44f9aa4c714">dc59c8d0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T19:55:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyensembl/-/commit/fcea494a8a8d5c7718141726359be9b731f92b58">fcea494a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T19:57:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#0c05e9e797806421ef921737ed1798eaaacf1491">
pyensembl.egg-info/PKG-INFO
</a>
</li>
<li class="file-stats">
<a href="#f9947d028acb12014b8dca78719cdb3cec24958c">
pyensembl/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#f14083a0e7ff065f2ec26ddda2d3029958307d89">
pyensembl/ensembl_release_versions.py
</a>
</li>
<li class="file-stats">
<a href="#6a4a2d20c84b34b39cc50eff81a2ee3069bb7964">
pyensembl/species.py
</a>
</li>
<li class="file-stats">
<a href="#e4f90a33e861e6a2e9f8ef480bf6176ac9605eba">
pyensembl/transcript.py
</a>
</li>
<li class="file-stats">
<a href="#047156d962434e888f88fa6a0b1e21d237fb8913">
test/test_transcript_ids.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 2.1</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: pyensembl</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.9.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.9.<span class="idiff left right">4</span></span>
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4
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Python interface to ensembl reference genome metadata</span>
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<td class="old_line diff-line-num" data-linenumber="5" 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="LC5" class="line" lang="plaintext">Home-page: https://github.com/openvax/pyensembl</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Alex Rubinsteyn</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: alex.rubinsteyn@unc.edu</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: http://www.apache.org/licenses/LICENSE-2.0.html</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Description: <a href="https://travis-ci.org/openvax/pyensembl"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> <img src="https://travis-ci.org/openvax/pyensembl.svg?branch=master" alt="Build Status" /></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> <a href="https://coveralls.io/github/openvax/pyensembl?branch=master"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> <a href="https://pypi.python.org/pypi/pyensembl/"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> PyEnsembl</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> =======</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files. </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> # Example Usage</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ```python</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> from pyensembl import EnsemblRelease</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> # release 77 uses human reference genome GRCh38</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> data = EnsemblRelease(77)</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> # will return ['HLA-A']</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> # get all exons associated with HLA-A</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> exon_ids = data.exon_ids_of_gene_name('HLA-A')</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> # Installation</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> ```sh</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> pip install pyensembl</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> [BioPython](http://biopython.org/).</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> Before using PyEnsembl, run the following command to download and install</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> Ensembl data:</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> pyensembl install --release <list of Ensembl release numbers> --species <species-name></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> ```</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"> For example, `pyensembl install --release 75 76 --species human` will download and install all</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> human reference data from Ensembl releases 75 and 76.</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"> Alternatively, you can create the `EnsemblRelease` object from inside a Python</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> process and call `ensembl_object.download()` followed by `ensembl_object.index()`.</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> ## Cache Location</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> By default, PyEnsembl uses the platform-specific `Cache` folder</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> and caches the files into the `pyensembl` sub-directory.</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> as your preferred location for caching:</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> ```sh</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> export PYENSEMBL_CACHE_DIR=/custom/cache/dir</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> or</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> ```python</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> import os</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> # ... PyEnsembl API usage</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> # Non-Ensembl Data</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> PyEnsembl also allows arbitrary genomes via the specification</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> of local file paths or remote URLs to both Ensembl and non-Ensembl GTF</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> and FASTA files. (Warning: GTF formats can vary, and handling of</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"> non-Ensembl data is still very much in development.)</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"> For example:</span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"> ```python</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> data = Genome(</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> reference_name='GRCh38',</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> annotation_name='my_genome_features',</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"> gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf')</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"> # parse GTF and construct database of genomic features</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext"> data.index()</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext"> gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"> # API</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> The `EnsemblRelease` object has methods to let you access all possible</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"> combinations of the annotation features *gene\_name*, *gene\_id*,</span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext"> *transcript\_name*, *transcript\_id*, *exon\_id* as well as the location of</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"> these genomic elements (contig, start position, end position, strand).</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> ## Genes</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"> <dl></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> <dt>genes(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> <dd>Returns a list of Gene objects, optionally restricted to a particular contig</span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"> or strand.</dd></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext"> <dt>genes_at_locus(contig, position, end=None, strand=None)</dt></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"> <dd>Returns a list of Gene objects overlapping a particular position on a contig,</span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext"> optionally extend into a range with the end parameter and restrict to</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"> forward or backward strand by passing strand='+' or strand='-'.</dd></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"> <dt>gene_by_id(gene_id)</dt></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"> <dd>Return a Gene object for given Ensembl gene ID (e.g. "ENSG00000068793").</dd></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext"> <dt>gene_names(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext"> <dd>Returns all gene names in the annotation database, optionally restricted</span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext"> to a particular contig or strand.</dd></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"> <dt>genes_by_name(gene_name)</dt></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext"> <dd>Get all the unqiue genes with the given name (there might be multiple</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"> due to copies in the genome), return a list containing a Gene object for each</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext"> distinct ID.</dd></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext"> </span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"> <dt>gene_by_protein_id(protein_id)</dt></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> <dd>Find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")</dd></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext"> </span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> <dt>gene_names_at_locus(contig, position, end=None, strand=None)</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"> </dt></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"> <dd>Names of genes overlapping with the given locus, optionally restricted by strand.</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> (returns a list to account for overlapping genes)</dd></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> <dt>gene_name_of_gene_id(gene_id)</span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"> </dt></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"> <dd>Returns name of gene with given genen ID.</dd></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"> </span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext"> <dt>gene_name_of_transcript_id(transcript_id)</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"> </dt><dd>Returns name of gene associated with given transcript ID.</dd></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"> </span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext"> <dt>gene_name_of_transcript_name(transcript_name)</span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"> </dt></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"> <dd>Returns name of gene associated with given transcript name.</dd></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"> <dt>gene_name_of_exon_id(exon_id)</span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"> </dt><dd>Returns name of gene associated with given exon ID.</dd></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext"> <dt>gene_ids(contig=None, strand=None)</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"> </dt></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext"> <dd>Return all gene IDs in the annotation database, optionally restricted by</span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext"> chromosome name or strand.</dd></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext"> </span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext"> <dt>gene_ids_of_gene_name(gene_name)</span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"> </dt></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"> <dd>Returns all Ensembl gene IDs with the given name.</dd></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"> </dl></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"> ## Transcripts</span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"> <dl></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext"> <dt>transcripts(contig=None, strand=None)</dt></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext"> <dd>Returns a list of Transcript objects for all transcript entries in the</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext"> Ensembl database, optionally restricted to a particular contig or strand.</dd></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext"> </span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext"> <dt>transcript_by_id(transcript_id)</dt></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext"> <dd>Construct a Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")</dd></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext"> </span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext"> <dt>transcripts_by_name(transcript_name)</dt></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext"> <dd>Returns a list of Transcript objects for every transcript matching the given name.</dd></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext"> <dt>transcript_names(contig=None, strand=None)</dt></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext"> <dd>Returns all transcript names in the annotation database.</dd></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext"> </span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> <dt>transcript_ids(contig=None, strand=None)</dt></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> <dd>Returns all transcript IDs in the annotation database.</dd></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext"> </span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"> <dt>transcript_ids_of_gene_id(gene_id)</dt></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext"> <dd>Return IDs of all transcripts associated with given gene ID.</dd></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext"> </span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"> <dt>transcript_ids_of_gene_name(gene_name)</dt></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext"> <dd>Return IDs of all transcripts associated with given gene name.</dd></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext"> </span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext"> <dt>transcript_ids_of_transcript_name(transcript_name)</dt></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext"> <dd>Find all Ensembl transcript IDs with the given name.</dd></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext"> </span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext"> <dt>transcript_ids_of_exon_id(exon_id)</dt></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext"> <dd>Return IDs of all transcripts associatd with given exon ID.</dd></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext"> </dl></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext"> </span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext"> ## Exons</span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext"> </span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext"> <dl></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext"> <dt>exon_ids(contig=None, strand=None)</dt></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext"> <dd>Returns a list of exons IDs in the annotation database, optionally restricted</span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext"> by the given chromosome and strand.</dd></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"> <dt>exon_ids_of_gene_id(gene_id)</dt></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given gene ID.</dd></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext"> <dt>exon_ids_of_gene_name(gene_name)</dt></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given gene name.</dd></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext"> <dt>exon_ids_of_transcript_id(transcript_id)</dt></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given transcript ID.</dd></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext"> <dt>exon_ids_of_transcript_name(transcript_name)</dt></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given transcript name.</dd></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext"> </dl></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Platform: UNKNOWN</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Classifier: Development Status :: 3 - Alpha</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Classifier: Environment :: Console</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">@@ -223,3 +15,217 @@ Classifier: License :: OSI Approved :: Apache Software License</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Classifier: Programming Language :: Python</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">License-File: LICENSE</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"><a href="https://app.travis-ci.com/github/openvax/pyensembl"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">PyEnsembl</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">=======</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files. </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"># Example Usage</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">```python</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">from pyensembl import EnsemblRelease</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"># release 77 uses human reference genome GRCh38</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">data = EnsemblRelease(77)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"># will return ['HLA-A']</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"># get all exons associated with HLA-A</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">exon_ids = data.exon_ids_of_gene_name('HLA-A')</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"># Installation</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">```sh</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">pip install pyensembl</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"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">[BioPython](http://biopython.org/).</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Before using PyEnsembl, run the following command to download and install</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Ensembl data:</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">pyensembl install --release <list of Ensembl release numbers> --species <species-name></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">For example, `pyensembl install --release 75 76 --species human` will download and install all</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">human reference data from Ensembl releases 75 and 76.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Alternatively, you can create the `EnsemblRelease` object from inside a Python</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">process and call `ensembl_object.download()` followed by `ensembl_object.index()`.</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">## Cache Location</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">By default, PyEnsembl uses the platform-specific `Cache` folder</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">and caches the files into the `pyensembl` sub-directory.</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">as your preferred location for caching:</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">```sh</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">export PYENSEMBL_CACHE_DIR=/custom/cache/dir</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">```</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">or</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">```python</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">import os</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"># ... PyEnsembl API usage</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">```</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"># Non-Ensembl Data</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">PyEnsembl also allows arbitrary genomes via the specification</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">of local file paths or remote URLs to both Ensembl and non-Ensembl GTF</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">and FASTA files. (Warning: GTF formats can vary, and handling of</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">non-Ensembl data is still very much in development.)</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">For example:</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">```python</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">data = Genome(</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> reference_name='GRCh38',</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> annotation_name='my_genome_features',</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf')</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"># parse GTF and construct database of genomic features</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">data.index()</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"># API</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">The `EnsemblRelease` object has methods to let you access all possible</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">combinations of the annotation features *gene\_name*, *gene\_id*,</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">*transcript\_name*, *transcript\_id*, *exon\_id* as well as the location of</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">these genomic elements (contig, start position, end position, strand).</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">## Genes</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"><dl></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"><dt>genes(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"><dd>Returns a list of Gene objects, optionally restricted to a particular contig</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">or strand.</dd></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"><dt>genes_at_locus(contig, position, end=None, strand=None)</dt></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"><dd>Returns a list of Gene objects overlapping a particular position on a contig,</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">optionally extend into a range with the end parameter and restrict to</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">forward or backward strand by passing strand='+' or strand='-'.</dd></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"><dt>gene_by_id(gene_id)</dt></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"><dd>Return a Gene object for given Ensembl gene ID (e.g. "ENSG00000068793").</dd></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"><dt>gene_names(contig=None, strand=None)</dt></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"><dd>Returns all gene names in the annotation database, optionally restricted</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">to a particular contig or strand.</dd></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"><dt>genes_by_name(gene_name)</dt></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"><dd>Get all the unqiue genes with the given name (there might be multiple</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">due to copies in the genome), return a list containing a Gene object for each</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">distinct ID.</dd></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"><dt>gene_by_protein_id(protein_id)</dt></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"><dd>Find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")</dd></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"><dt>gene_names_at_locus(contig, position, end=None, strand=None)</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"></dt></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"><dd>Names of genes overlapping with the given locus, optionally restricted by strand.</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">(returns a list to account for overlapping genes)</dd></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"><dt>gene_name_of_gene_id(gene_id)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></dt></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"><dd>Returns name of gene with given genen ID.</dd></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"><dt>gene_name_of_transcript_id(transcript_id)</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></dt><dd>Returns name of gene associated with given transcript ID.</dd></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"><dt>gene_name_of_transcript_name(transcript_name)</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"></dt></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"><dd>Returns name of gene associated with given transcript name.</dd></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"><dt>gene_name_of_exon_id(exon_id)</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"></dt><dd>Returns name of gene associated with given exon ID.</dd></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"><dt>gene_ids(contig=None, strand=None)</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></dt></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"><dd>Return all gene IDs in the annotation database, optionally restricted by</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">chromosome name or strand.</dd></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"><dt>gene_ids_of_gene_name(gene_name)</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"></dt></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"><dd>Returns all Ensembl gene IDs with the given name.</dd></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"></dl></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">## Transcripts</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"><dl></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"><dt>transcripts(contig=None, strand=None)</dt></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"><dd>Returns a list of Transcript objects for all transcript entries in the</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">Ensembl database, optionally restricted to a particular contig or strand.</dd></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"><dt>transcript_by_id(transcript_id)</dt></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"><dd>Construct a Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")</dd></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"><dt>transcripts_by_name(transcript_name)</dt></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"><dd>Returns a list of Transcript objects for every transcript matching the given name.</dd></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"><dt>transcript_names(contig=None, strand=None)</dt></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"><dd>Returns all transcript names in the annotation database.</dd></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"><dt>transcript_ids(contig=None, strand=None)</dt></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"><dd>Returns all transcript IDs in the annotation database.</dd></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"><dt>transcript_ids_of_gene_id(gene_id)</dt></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"><dd>Return IDs of all transcripts associated with given gene ID.</dd></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"><dt>transcript_ids_of_gene_name(gene_name)</dt></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"><dd>Return IDs of all transcripts associated with given gene name.</dd></span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
</pre>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"><dt>transcript_ids_of_transcript_name(transcript_name)</dt></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"><dd>Find all Ensembl transcript IDs with the given name.</dd></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"><dt>transcript_ids_of_exon_id(exon_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"><dd>Return IDs of all transcripts associatd with given exon ID.</dd></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"></dl></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">## Exons</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"><dl></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"><dt>exon_ids(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"><dd>Returns a list of exons IDs in the annotation database, optionally restricted</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">by the given chromosome and strand.</dd></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"><dt>exon_by_id(exon_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"><dd>Construct an Exon object for given Ensembl exon ID (e.g. "ENSE00001209410")</dd></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"><dt>exon_ids_of_gene_id(gene_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given gene ID.</dd></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"><dt>exon_ids_of_gene_name(gene_name)</dt></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given gene name.</dd></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"><dt>exon_ids_of_transcript_id(transcript_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given transcript ID.</dd></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"><dt>exon_ids_of_transcript_name(transcript_name)</dt></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given transcript name.</dd></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"></dl></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://travis-ci.<span class="idiff left right">org</span>/openvax/pyensembl"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://travis-ci.<span class="idiff left right">org</span>/openvax/pyensembl.svg?branch=master"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Build Status"</span> <span class="nt" style="color: #000080;">/></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://<span class="idiff left">app.</span>travis-ci.<span class="idiff right">com/github</span>/openvax/pyensembl"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://coveralls.io/github/openvax/pyensembl?branch=master"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://coveralls.io/repos/openvax/pyensembl/badge.svg?branch=master&service=github"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"Coverage Status"</span> <span class="nt" style="color: #000080;">/></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">@@ -193,6 +193,9 @@ Ensembl database, optionally restricted to a particular contig or strand.</dd></td>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown"><span class="nt" style="color: #000080;"><dd></span>Returns a list of exons IDs in the annotation database, optionally restricted</span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown">by the given chromosome and strand.<span class="nt" style="color: #000080;"></dd></span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"><span class="nt" style="color: #000080;"><dt></span>exon_by_id(exon_id)<span class="nt" style="color: #000080;"></dt></span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="markdown"><span class="nt" style="color: #000080;"><dd></span>Construct an Exon object for given Ensembl exon ID (e.g. "ENSE00001209410")<span class="nt" style="color: #000080;"></dd></span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown"><span class="nt" style="color: #000080;"><dt></span>exon_ids_of_gene_id(gene_id)<span class="nt" style="color: #000080;"></dt></span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="markdown"><span class="nt" style="color: #000080;"><dd></span>Returns a list of exon IDs associated with a given gene ID.<span class="nt" style="color: #000080;"></dd></span></span>
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<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pyensembl (1.9.4+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 11 Oct 2021 19:56:10 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">pyensembl (1.9.1+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Steffen Moeller, Nilesh Patra ]</span>
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<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> python3-gtfparse</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># python3-tinytimer # only run during tests that are not run because of</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"># demand for internet access</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: https://github.com/openvax/pyensembl</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pyensembl</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pyensembl.git</span>
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<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#0c05e9e797806421ef921737ed1798eaaacf1491"><strong>pyensembl.egg-info/PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 2.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: pyensembl</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.9.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.9.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Python interface to ensembl reference genome metadata</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/openvax/pyensembl</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Alex Rubinsteyn</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: alex.rubinsteyn@unc.edu</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: http://www.apache.org/licenses/LICENSE-2.0.html</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Description: <a href="https://travis-ci.org/openvax/pyensembl"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> <img src="https://travis-ci.org/openvax/pyensembl.svg?branch=master" alt="Build Status" /></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> </a></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> <a href="https://coveralls.io/github/openvax/pyensembl?branch=master"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> <img src="https://coveralls.io/repos/openvax/pyensembl/badge.svg?branch=master&service=github" alt="Coverage Status" /></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> </a></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> <a href="https://pypi.python.org/pypi/pyensembl/"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> <img src="https://img.shields.io/pypi/v/pyensembl.svg?maxAge=1000" alt="PyPI" /></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> PyEnsembl</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> =======</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files. </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> # Example Usage</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ```python</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> from pyensembl import EnsemblRelease</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> # release 77 uses human reference genome GRCh38</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> data = EnsemblRelease(77)</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> # will return ['HLA-A']</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> # get all exons associated with HLA-A</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> exon_ids = data.exon_ids_of_gene_name('HLA-A')</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> # Installation</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> ```sh</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> pip install pyensembl</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> [BioPython](http://biopython.org/).</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> Before using PyEnsembl, run the following command to download and install</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> Ensembl data:</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> pyensembl install --release <list of Ensembl release numbers> --species <species-name></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> ```</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"> For example, `pyensembl install --release 75 76 --species human` will download and install all</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> human reference data from Ensembl releases 75 and 76.</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"> Alternatively, you can create the `EnsemblRelease` object from inside a Python</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> process and call `ensembl_object.download()` followed by `ensembl_object.index()`.</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> ## Cache Location</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> By default, PyEnsembl uses the platform-specific `Cache` folder</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> and caches the files into the `pyensembl` sub-directory.</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> as your preferred location for caching:</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> ```sh</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> export PYENSEMBL_CACHE_DIR=/custom/cache/dir</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> or</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> ```python</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> import os</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> # ... PyEnsembl API usage</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> # Non-Ensembl Data</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> PyEnsembl also allows arbitrary genomes via the specification</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> of local file paths or remote URLs to both Ensembl and non-Ensembl GTF</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> and FASTA files. (Warning: GTF formats can vary, and handling of</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"> non-Ensembl data is still very much in development.)</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"> For example:</span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"> ```python</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> data = Genome(</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> reference_name='GRCh38',</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> annotation_name='my_genome_features',</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"> gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf')</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"> # parse GTF and construct database of genomic features</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext"> data.index()</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext"> gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"> ```</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"> # API</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> The `EnsemblRelease` object has methods to let you access all possible</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"> combinations of the annotation features *gene\_name*, *gene\_id*,</span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext"> *transcript\_name*, *transcript\_id*, *exon\_id* as well as the location of</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"> these genomic elements (contig, start position, end position, strand).</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> ## Genes</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"> <dl></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> <dt>genes(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> <dd>Returns a list of Gene objects, optionally restricted to a particular contig</span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"> or strand.</dd></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext"> <dt>genes_at_locus(contig, position, end=None, strand=None)</dt></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"> <dd>Returns a list of Gene objects overlapping a particular position on a contig,</span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext"> optionally extend into a range with the end parameter and restrict to</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"> forward or backward strand by passing strand='+' or strand='-'.</dd></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"> <dt>gene_by_id(gene_id)</dt></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"> <dd>Return a Gene object for given Ensembl gene ID (e.g. "ENSG00000068793").</dd></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext"> <dt>gene_names(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext"> <dd>Returns all gene names in the annotation database, optionally restricted</span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext"> to a particular contig or strand.</dd></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"> <dt>genes_by_name(gene_name)</dt></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext"> <dd>Get all the unqiue genes with the given name (there might be multiple</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"> due to copies in the genome), return a list containing a Gene object for each</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext"> distinct ID.</dd></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"> <dt>gene_by_protein_id(protein_id)</dt></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> <dd>Find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")</dd></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext"> </span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> <dt>gene_names_at_locus(contig, position, end=None, strand=None)</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"> </dt></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"> <dd>Names of genes overlapping with the given locus, optionally restricted by strand.</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> (returns a list to account for overlapping genes)</dd></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> <dt>gene_name_of_gene_id(gene_id)</span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"> </dt></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"> <dd>Returns name of gene with given genen ID.</dd></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"> </span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext"> <dt>gene_name_of_transcript_id(transcript_id)</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"> </dt><dd>Returns name of gene associated with given transcript ID.</dd></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"> </span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext"> <dt>gene_name_of_transcript_name(transcript_name)</span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"> </dt></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"> <dd>Returns name of gene associated with given transcript name.</dd></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext"> </span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"> <dt>gene_name_of_exon_id(exon_id)</span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"> </dt><dd>Returns name of gene associated with given exon ID.</dd></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext"> </span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext"> <dt>gene_ids(contig=None, strand=None)</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"> </dt></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext"> <dd>Return all gene IDs in the annotation database, optionally restricted by</span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext"> chromosome name or strand.</dd></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext"> </span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext"> <dt>gene_ids_of_gene_name(gene_name)</span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"> </dt></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"> <dd>Returns all Ensembl gene IDs with the given name.</dd></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext"> </span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"> </dl></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext"> </span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"> ## Transcripts</span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext"> </span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"> <dl></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext"> <dt>transcripts(contig=None, strand=None)</dt></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext"> <dd>Returns a list of Transcript objects for all transcript entries in the</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext"> Ensembl database, optionally restricted to a particular contig or strand.</dd></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext"> </span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext"> <dt>transcript_by_id(transcript_id)</dt></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext"> <dd>Construct a Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")</dd></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext"> </span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext"> <dt>transcripts_by_name(transcript_name)</dt></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext"> <dd>Returns a list of Transcript objects for every transcript matching the given name.</dd></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext"> </span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext"> <dt>transcript_names(contig=None, strand=None)</dt></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext"> <dd>Returns all transcript names in the annotation database.</dd></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext"> </span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> <dt>transcript_ids(contig=None, strand=None)</dt></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> <dd>Returns all transcript IDs in the annotation database.</dd></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext"> </span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"> <dt>transcript_ids_of_gene_id(gene_id)</dt></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext"> <dd>Return IDs of all transcripts associated with given gene ID.</dd></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext"> </span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"> <dt>transcript_ids_of_gene_name(gene_name)</dt></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext"> <dd>Return IDs of all transcripts associated with given gene name.</dd></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext"> </span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext"> <dt>transcript_ids_of_transcript_name(transcript_name)</dt></span>
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<td class="old_line diff-line-num old" data-linenumber="191" 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">
191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext"> <dd>Find all Ensembl transcript IDs with the given name.</dd></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext"> <dt>transcript_ids_of_exon_id(exon_id)</dt></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext"> <dd>Return IDs of all transcripts associatd with given exon ID.</dd></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext"> </dl></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext"> ## Exons</span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext"> <dl></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext"> <dt>exon_ids(contig=None, strand=None)</dt></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext"> <dd>Returns a list of exons IDs in the annotation database, optionally restricted</span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext"> by the given chromosome and strand.</dd></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"> <dt>exon_ids_of_gene_id(gene_id)</dt></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given gene ID.</dd></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext"> <dt>exon_ids_of_gene_name(gene_name)</dt></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given gene name.</dd></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext"> <dt>exon_ids_of_transcript_id(transcript_id)</dt></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given transcript ID.</dd></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext"> <dt>exon_ids_of_transcript_name(transcript_name)</dt></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="plaintext"> <dd>Returns a list of exon IDs associated with a given transcript name.</dd></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext"> </dl></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Platform: UNKNOWN</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Classifier: Development Status :: 3 - Alpha</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Classifier: Environment :: Console</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">@@ -223,3 +15,217 @@ Classifier: License :: OSI Approved :: Apache Software License</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Classifier: Programming Language :: Python</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Description-Content-Type: text/markdown</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">License-File: LICENSE</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"><a href="https://app.travis-ci.com/github/openvax/pyensembl"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> <img src="https://app.travis-ci.com/openvax/pyensembl.svg?branch=master" alt="Build Status" /></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></a></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"><a href="https://coveralls.io/github/openvax/pyensembl?branch=master"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> <img src="https://coveralls.io/repos/openvax/pyensembl/badge.svg?branch=master&service=github" alt="Coverage Status" /></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pyensembl/"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> <img src="https://img.shields.io/pypi/v/pyensembl.svg?maxAge=1000" alt="PyPI" /></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">PyEnsembl</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">=======</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files. </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"># Example Usage</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">```python</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">from pyensembl import EnsemblRelease</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"># release 77 uses human reference genome GRCh38</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">data = EnsemblRelease(77)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"># will return ['HLA-A']</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"># get all exons associated with HLA-A</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">exon_ids = data.exon_ids_of_gene_name('HLA-A')</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"># Installation</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">```sh</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">pip install pyensembl</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"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">This should also install any required packages, such as [datacache](https://github.com/openvax/datacache) and</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">[BioPython](http://biopython.org/).</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Before using PyEnsembl, run the following command to download and install</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Ensembl data:</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">```</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">pyensembl install --release <list of Ensembl release numbers> --species <species-name></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">```</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">For example, `pyensembl install --release 75 76 --species human` will download and install all</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">human reference data from Ensembl releases 75 and 76.</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Alternatively, you can create the `EnsemblRelease` object from inside a Python</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">process and call `ensembl_object.download()` followed by `ensembl_object.index()`.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">## Cache Location</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">By default, PyEnsembl uses the platform-specific `Cache` folder</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">and caches the files into the `pyensembl` sub-directory.</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">as your preferred location for caching:</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">```sh</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">export PYENSEMBL_CACHE_DIR=/custom/cache/dir</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">```</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">or</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">```python</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">import os</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"># ... PyEnsembl API usage</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">```</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"># Non-Ensembl Data</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">PyEnsembl also allows arbitrary genomes via the specification</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">of local file paths or remote URLs to both Ensembl and non-Ensembl GTF</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">and FASTA files. (Warning: GTF formats can vary, and handling of</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">non-Ensembl data is still very much in development.)</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">For example:</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">```python</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">data = Genome(</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> reference_name='GRCh38',</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> annotation_name='my_genome_features',</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf')</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"># parse GTF and construct database of genomic features</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">data.index()</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">gene_names = data.gene_names_at_locus(contig=6, position=29945884)</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">```</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"># API</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">The `EnsemblRelease` object has methods to let you access all possible</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">combinations of the annotation features *gene\_name*, *gene\_id*,</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">*transcript\_name*, *transcript\_id*, *exon\_id* as well as the location of</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">these genomic elements (contig, start position, end position, strand).</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">## Genes</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"><dl></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"><dt>genes(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"><dd>Returns a list of Gene objects, optionally restricted to a particular contig</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">or strand.</dd></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"><dt>genes_at_locus(contig, position, end=None, strand=None)</dt></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"><dd>Returns a list of Gene objects overlapping a particular position on a contig,</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">optionally extend into a range with the end parameter and restrict to</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">forward or backward strand by passing strand='+' or strand='-'.</dd></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"><dt>gene_by_id(gene_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"><dd>Return a Gene object for given Ensembl gene ID (e.g. "ENSG00000068793").</dd></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"><dt>gene_names(contig=None, strand=None)</dt></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"><dd>Returns all gene names in the annotation database, optionally restricted</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">to a particular contig or strand.</dd></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"><dt>genes_by_name(gene_name)</dt></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"><dd>Get all the unqiue genes with the given name (there might be multiple</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">due to copies in the genome), return a list containing a Gene object for each</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">distinct ID.</dd></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"><dt>gene_by_protein_id(protein_id)</dt></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"><dd>Find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")</dd></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"><dt>gene_names_at_locus(contig, position, end=None, strand=None)</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"></dt></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"><dd>Names of genes overlapping with the given locus, optionally restricted by strand.</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">(returns a list to account for overlapping genes)</dd></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"><dt>gene_name_of_gene_id(gene_id)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></dt></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"><dd>Returns name of gene with given genen ID.</dd></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"><dt>gene_name_of_transcript_id(transcript_id)</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></dt><dd>Returns name of gene associated with given transcript ID.</dd></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"><dt>gene_name_of_transcript_name(transcript_name)</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"></dt></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"><dd>Returns name of gene associated with given transcript name.</dd></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"><dt>gene_name_of_exon_id(exon_id)</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"></dt><dd>Returns name of gene associated with given exon ID.</dd></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"><dt>gene_ids(contig=None, strand=None)</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></dt></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"><dd>Return all gene IDs in the annotation database, optionally restricted by</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">chromosome name or strand.</dd></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"><dt>gene_ids_of_gene_name(gene_name)</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"></dt></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"><dd>Returns all Ensembl gene IDs with the given name.</dd></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"></dl></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">## Transcripts</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"><dl></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"><dt>transcripts(contig=None, strand=None)</dt></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"><dd>Returns a list of Transcript objects for all transcript entries in the</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">Ensembl database, optionally restricted to a particular contig or strand.</dd></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>
</pre>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"><dt>transcript_by_id(transcript_id)</dt></span>
</pre>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"><dd>Construct a Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")</dd></span>
</pre>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"></span>
</pre>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"><dt>transcripts_by_name(transcript_name)</dt></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"><dd>Returns a list of Transcript objects for every transcript matching the given name.</dd></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"></span>
</pre>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"><dt>transcript_names(contig=None, strand=None)</dt></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"><dd>Returns all transcript names in the annotation database.</dd></span>
</pre>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"></span>
</pre>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"><dt>transcript_ids(contig=None, strand=None)</dt></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"><dd>Returns all transcript IDs in the annotation database.</dd></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"><dt>transcript_ids_of_gene_id(gene_id)</dt></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"><dd>Return IDs of all transcripts associated with given gene ID.</dd></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"><dt>transcript_ids_of_gene_name(gene_name)</dt></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"><dd>Return IDs of all transcripts associated with given gene name.</dd></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"><dt>transcript_ids_of_transcript_name(transcript_name)</dt></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"><dd>Find all Ensembl transcript IDs with the given name.</dd></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"><dt>transcript_ids_of_exon_id(exon_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"><dd>Return IDs of all transcripts associatd with given exon ID.</dd></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"></dl></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">## Exons</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"><dl></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"><dt>exon_ids(contig=None, strand=None)</dt></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"><dd>Returns a list of exons IDs in the annotation database, optionally restricted</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">by the given chromosome and strand.</dd></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"><dt>exon_by_id(exon_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"><dd>Construct an Exon object for given Ensembl exon ID (e.g. "ENSE00001209410")</dd></span>
</pre>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"><dt>exon_ids_of_gene_id(gene_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given gene ID.</dd></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"><dt>exon_ids_of_gene_name(gene_name)</dt></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given gene name.</dd></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"><dt>exon_ids_of_transcript_id(transcript_id)</dt></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given transcript ID.</dd></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"><dt>exon_ids_of_transcript_name(transcript_name)</dt></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"><dd>Returns a list of exon IDs associated with a given transcript name.</dd></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"></dl></span>
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<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#f9947d028acb12014b8dca78719cdb3cec24958c"><strong>pyensembl/__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">@@ -40,7 +40,7 @@ from .species import (</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.transcript</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Transcript</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">'1.9.<span class="idiff left right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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;">'1.9.<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"MemoryCache"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#f14083a0e7ff065f2ec26ddda2d3029958307d89"><strong>pyensembl/ensembl_release_versions.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">@@ -13,7 +13,7 @@</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">MIN_ENSEMBL_RELEASE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">54</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">MAX_ENSEMBL_RELEASE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10<span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">MAX_ENSEMBL_RELEASE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_release_number</span><span class="p">(</span><span class="n" style="color: #333;">release</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#6a4a2d20c84b34b39cc50eff81a2ee3069bb7964"><strong>pyensembl/species.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">@@ -177,8 +177,8 @@ mouse = Species.register(</td>
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">synonyms</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"mouse"</span><span class="p">,</span> <span class="s" style="color: #d14;">"house mouse"</span><span class="p">],</span></span>
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">reference_assemblies</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"NCBIM37"</span><span class="p">:</span> <span class="p">(</span><span class="mi" style="color: #099;">54</span><span class="p">,</span> <span class="mi" style="color: #099;">67</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">"GRCm38"</span><span class="p">:</span> <span class="p">(</span><span class="mi" style="color: #099;">68</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">MAX_ENSEMBL_RELEASE</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">"GRCm38"</span><span class="p">:</span> <span class="p">(</span><span class="mi" style="color: #099;">68</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">102</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="s" style="color: #d14;">"GRCm39"</span><span class="p">:</span> <span class="p">(</span><span class="mi" style="color: #099;">103</span><span class="p">,</span> <span class="n" style="color: #333;">MAX_ENSEMBL_RELEASE</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"><span class="n" style="color: #333;">dog</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Species</span><span class="p">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#e4f90a33e861e6a2e9f8ef480bf6176ac9605eba"><strong>pyensembl/transcript.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">@@ -418,7 +418,7 @@ class Transcript(LocusWithGenome):</td>
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"><span class="s" style="color: #d14;"> Spliced cDNA sequence of transcript</span></span>
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419
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"><span class="s" style="color: #d14;"> (includes 5" UTR, coding sequence, and 3" UTR)</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">transcript_sequences</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">id</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">transcript_sequences</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">transcript_id</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rsplit</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"."</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">memoized_property</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">first_start_codon_spliced_offset</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/pyensembl/-/compare/320510e2d1b892149d8b5b5932a90a599fae22e4...fcea494a8a8d5c7718141726359be9b731f92b58#047156d962434e888f88fa6a0b1e21d237fb8913"><strong>test/test_transcript_ids.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" 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">@@ -50,8 +50,9 @@ def test_all_transcript_ids(ensembl):</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"Missing transcript ID %s from %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_id</span><span class="p">,</span> <span class="n" style="color: #333;">ensembl</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_transcript_id_of_protein_id_CCR2</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># looked up CCR2-201 transcript ID ENST00000292301 mapping to protein ID</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ENSP00000292301 on Sept. 14th 2016 from GRCh38 Ensembl release 85</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Looked up on Oct 9 2021:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CCR2-203 ENST00000445132.3 maps to ENSP00000399285.2</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Ensembl release 104, GRCh38.p13</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">transcript_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grch38</span><span class="p">.</span><span class="n" style="color: #333;">transcript_id_of_protein_id</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"ENSP00000<span class="idiff left right">292301</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">eq_</span><span class="p">(</span><span class="s" style="color: #d14;">"ENST00000<span class="idiff left right">292301</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">transcript_id</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="s" style="color: #d14;">"ENSP00000<span class="idiff left right">399285</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">eq_</span><span class="p">(</span><span class="s" style="color: #d14;">"ENST00000<span class="idiff left right">445132</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">transcript_id</span><span class="p">)</span></span></pre>
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