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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/changeo">Debian Med / changeo</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825">fc08a33f</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-15T13:05:08+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.1</pre>
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<h4>13 changed files:</h4>
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<li class="file-stats">
<a href="#3374c1c18de688d968548dc001e40ee700f04f6f">
INSTALL.rst
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<li class="file-stats">
<a href="#8e9983d68bc118797b12e3c989281a14e4ae4a62">
NEWS.rst
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<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#4a383f2b81fca82a50ea8a84941881de21634cb0">
bin/ConvertDb.py
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<li class="file-stats">
<a href="#4a67c1d67f8e61dd1fa3d6d72a4109982d66b724">
bin/DefineClones.py
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<li class="file-stats">
<a href="#b07d9f16b53c7bf45411d329e0d2defdd381c644">
bin/ParseDb.py
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<li class="file-stats">
<a href="#644e37c5303095d9570d84c455cb6822d50aa50e">
changeo.egg-info/PKG-INFO
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<li class="file-stats">
<a href="#fa6955e3d60d7ec84bad39b05425d008283df3bc">
changeo.egg-info/SOURCES.txt
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<li class="file-stats">
<a href="#1f4dd37096d2ddfcb225023d881d7065285142c4">
changeo.egg-info/requires.txt
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<li class="file-stats">
<a href="#05fdcdf376e61bb9ea4aa991f73cfd29b5aa07b3">
changeo/IO.py
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<li class="file-stats">
<a href="#39d40dda335856b0a31785a995858f9160602e82">
changeo/Version.py
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<a href="#80b8baffe249ed1b18aa1e58fb5a921ea4e96247">
<span class="deleted-file">
−
changeo/data/receptor.tsv
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<h4>Changes:</h4>
<li id="3374c1c18de688d968548dc001e40ee700f04f6f">
<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#3374c1c18de688d968548dc001e40ee700f04f6f"><strong>INSTALL.rst</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,9 +5,9 @@ The simplest way to install the latest stable release of Change-O is via pip::</td>
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<td class="diff-line-num new_line" 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"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> > pip3 install changeo --user</span>
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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">The current development build can be installed using pip and <span class="idiff left right">mercurial</span> in similar fashion::</span>
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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">The current development build can be installed using pip and <span class="idiff left right">git</span> in similar fashion::</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> > pip3 install <span class="idiff left right">hg+https://bitbucket.org/kleinstein/changeo@default</span> --user</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> > pip3 install <span class="idiff left right">git+https://bitbucket.org/kleinstein/changeo@master</span> --user</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">If you currently have a development version installed, then you will likely</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext">need to add the arguments ``--upgrade --no-deps --force-reinstall`` to the</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,14 +16,20 @@ pip3 command.</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Requirements</span>
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext">--------------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">The minimum dependencies for installation are:</span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">+ `Python 3.4.0 <http://python.org>`__</span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext">+ `setuptools 2.0 <http://bitbucket.org/pypa/setuptools>`__</span>
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<td class="diff-line-num new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">+ `NumPy 1.8 <http://numpy.org>`__</span>
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<td class="diff-line-num old_line" data-linenumber="22" 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="LC24" class="line" lang="plaintext">+ `SciPy 0.14 <http://scipy.org>`__</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">+ `pandas 0.15 <http://pandas.pydata.org>`__</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">+ `Biopython 1.65 <http://biopython.org>`__</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">+ `presto 0.5.10 <http://presto.readthedocs.io>`__</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">+ `airr 1.2.1 <https://docs.airr-community.org>`__.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">+ `pandas 0.24 <http://pandas.pydata.org>`__</span>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">+ `Biopython 1.71 <http://biopython.org>`__</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">+ `presto 0.6.2 <http://presto.readthedocs.io>`__</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">+ `airr 1.2.1 <https://docs.airr-community.org>`__</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Some tools wrap external applications that are not required for installation.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Those tools require minimum versions of:</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">+ AlignRecords requires `MUSCLE 3.8 <http://www.drive5.com/muscle>`__</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">+ ConvertDb-genbank requires `tbl2asn <https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2>`__</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">+ AssignGenes requires `IgBLAST 1.6 <https://ncbi.github.io/igblast>`__, but</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" 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">@@ -39,7 +45,7 @@ Linux</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> Biopython according to its</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> `instructions <http://biopython.org/DIST/docs/install/Installation.html>`__.</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">2. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">2. Install `presto 0.5.<span class="idiff left right">1</span>0 <http://presto.readthedocs.io>`__ or greater.</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">3. Download the Change-O bundle and run::</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" 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">@@ -75,12 +81,12 @@ Mac OS X</td>
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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"> > brew install --env=std gfortran</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="LC78" class="line" lang="plaintext">7. Install NumPy, SciPy, pandas and Biopyton using the Python package</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">7. Install NumPy, SciPy, pandas and Biopyt<span class="idiff left right">h</span>on using the Python package</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> manager::</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> > pip3 install numpy scipy pandas biopython</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="LC83" class="line" lang="plaintext">8. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">8. Install `presto 0.5.<span class="idiff left right">1</span>0 <http://presto.readthedocs.io>`__ or greater.</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">9. Download the Change-O bundle, open a terminal window, change directories</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> to the download folder, and run::</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,7 +104,7 @@ Windows</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> `Unofficial Windows binary <http://www.lfd.uci.edu/~gohlke/pythonlibs>`__</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> collection.</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">3. Install `presto 0.5.0 <http://presto.readthedocs.io>`__ or greater.</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">3. Install `presto 0.5.<span class="idiff left right">1</span>0 <http://presto.readthedocs.io>`__ or greater.</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">4. Download the Change-O bundle, open a Command Prompt, change directories to</span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> the download folder, and run::</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,16 +114,16 @@ Windows</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">5. For a default installation of Python 3.4, the Change-0 scripts will be</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> installed into ``C:\Python34\Scripts`` and should be directly</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"> executable from the Command Prompt. If this is not the case, then</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> follow step <span class="idiff left right">5</span> below.</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> follow step <span class="idiff left right">6</span> below.</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">6. Add both the ``C:\Python34`` and ``C:\Python34\Scripts`` directories</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> to your ``%Path%``. On Windows 7 the ``%Path%`` setting is located</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> under Control Panel -> System and Security -> System -> Advanced</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> System Settings -> Environment variables -> System variables -> Path.</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"><span class="idiff left right">6</span>. If you have trouble with the ``.py`` file associations, try adding ``.PY``</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> to your ``PATHEXT`` environment variable. Also, opening a</span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"> <span class="idiff left right">command p</span>rompt as Administrator and run::</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"><span class="idiff left right">7</span>. If you have trouble with the ``.py`` file associations, try adding ``.PY``</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> to your ``PATHEXT`` environment variable. Also, <span class="idiff left right">try </span>opening a</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> <span class="idiff left right">Command P</span>rompt as Administrator and run::</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> > assoc .py=Python.File</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"> > ftype Python.File="C:\Python34\python.exe" "%1" %*</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Release Notes</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">===============================================================================</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Version 1.0.1: October 13, 2020</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">-------------------------------------------------------------------------------</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">+ Updated to support Biopython v1.78.</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">+ Increased the biopython dependency to v1.71.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">+ Increased the presto dependency to 0.6.2.</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Version 1.0.0: May 6, 2020</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">-------------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: changeo</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.0.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.0.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://changeo.readthedocs.io</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Namita Gupta, Jason Anthony Vander Heiden</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#4a383f2b81fca82a50ea8a84941881de21634cb0"><strong>bin/ConvertDb.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">@@ -20,7 +20,6 @@ from time import time</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Alphabet</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IUPAC</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Presto and changeo imports</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">presto.Annotation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">flattenAnnotation</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">@@ -70,7 +69,7 @@ def buildSeqRecord(db_record, id_field, seq_field, meta_fields=None):</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">desc_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flattenAnnotation</span><span class="p">(</span><span class="n" style="color: #333;">desc_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create SeqRecord</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">db_record</span><span class="p">[</span><span class="n" style="color: #333;">seq_field</span><span class="p">]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IUPAC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ambiguous_dna</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">db_record</span><span class="p">[</span><span class="n" style="color: #333;">seq_field</span><span class="p">]),</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">desc_str</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">desc_str</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq_record</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -787,8 +786,7 @@ def makeGenbankSequence(record, name=None, label=None, count_field=None, index_f</td>
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'%s [note=%s]'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">note</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Return SeqRecord and positions</span></span>
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">seq_start</span><span class="p">:</span><span class="n" style="color: #333;">seq_end</span><span class="p">],</span> <span class="n" style="color: #333;">IUPAC</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_dna</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">seq_start</span><span class="p">:</span><span class="n" style="color: #333;">seq_end</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'record'</span><span class="p">:</span> <span class="n" style="color: #333;">record</span><span class="p">,</span> <span class="s" style="color: #d14;">'start'</span><span class="p">:</span> <span class="n" style="color: #333;">seq_start</span><span class="p">,</span> <span class="s" style="color: #d14;">'end'</span><span class="p">:</span> <span class="n" style="color: #333;">seq_end</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</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">@@ -49,7 +49,7 @@ choices_distance_model = ('ham', 'aa', 'hh_s1f', 'hh_s5f',</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filterMissing</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">seq_field</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">junction_attr</span><span class="p">,</span> <span class="n" style="color: #333;">v_field</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">v_attr</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">j_field</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">j_attr</span><span class="p">,</span> <span class="n" style="color: #333;">max_missing</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_max_missing</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> Splits a set of sequence into passed and failed groups based on the number</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> Splits a set of sequence<span class="idiff left right">s</span> into passed and failed groups based on the number</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> of missing characters in the sequence</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:</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">@@ -60,7 +60,7 @@ def filterMissing(data, seq_field=junction_attr, v_field=v_attr,</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> max_missing (int): maximum number of missing characters (non-ACGT) to permit before failing the record.</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> changeo.Multiprocessing.DbResult : object<span class="idiff left right">ed</span> containing filtered records.</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> changeo.Multiprocessing.DbResult : object containing filtered records.</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Function to validate the sequence string</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_pass</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -266,17 +266,17 @@ def distanceClones(result, seq_field=default_junction_field, model=default_dista</td>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"><span class="s" style="color: #d14;"> Separates a set of Receptor objects into clones</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"><span class="s" style="color: #d14;"> result : a changeo.Multiprocessing.DbResult object with filtered records to clone</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;"> seq_field : sequence field used to calculate distance between records</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"><span class="s" style="color: #d14;"> model : substitution model used to calculate distance</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;"> distance : t<span class="idiff left right">he</span> distance threshold to assign clonal groups</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;"> distance : t<span class="idiff left right"> </span> distance threshold to assign clonal groups</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"><span class="s" style="color: #d14;"> dist_mat : pandas DataFrame of pairwise nucleotide or amino acid distances</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;"> norm : normalization method</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;"> sym : symmetry method</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;"> linkage : type of linkage</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"><span class="s" style="color: #d14;"> changeo.Multiprocessing.DbResult : an updated DbResult object</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get distance matrix if not provided</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">@@ -349,7 +349,7 @@ def collectQueue(alive, result_queue, collect_queue, db_file, fields,</td>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;"> Assembles results from a queue of individual sequence results and manages log/file I/O</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"><span class="s" style="color: #d14;"> alive = a multiprocessing.Value boolean controlling whether processing continues</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"><span class="s" style="color: #d14;"> if False exit process</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"><span class="s" style="color: #d14;"> result_queue : a multiprocessing.Queue holding processQueue results</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">@@ -556,7 +556,7 @@ def defineClones(db_file, seq_field=default_junction_field, v_field=default_v_fi</td>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">group_args</span><span class="p">[</span><span class="s" style="color: #d14;">'j_field'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j_field</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">feed_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'db_file'</span><span class="p">:</span> <span class="n" style="color: #333;">db_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"> <span class="s" style="color: #d14;">'reader'</span><span class="p">:</span> <span class="n" style="color: #333;">reader</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="s" style="color: #d14;">'group_func'</span><span class="p">:</span> <span class="n" style="color: #333;">group_func</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="s" style="color: #d14;">'group_func'</span><span class="p">:</span> <span class="n" style="color: #333;">group_func</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="s" style="color: #d14;">'group_args'</span><span class="p">:</span> <span class="n" style="color: #333;">group_args</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define worker function and arguments</span></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#b07d9f16b53c7bf45411d329e0d2defdd381c644"><strong>bin/ParseDb.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,7 +168,7 @@ def addDbFile(db_file, fields, values, out_file=None, out_args=default_out_args)</td>
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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'VALUES'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">printLog</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">)</span></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Open inut</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Open in<span class="idiff left right">p</span>ut</span></span>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">db_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">db_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">db_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TSVReader</span><span class="p">(</span><span class="n" style="color: #333;">db_handle</span><span class="p">)</span></span>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">__</span><span class="p">,</span> <span class="n" style="color: #333;">__</span><span class="p">,</span> <span class="n" style="color: #333;">out_args</span><span class="p">[</span><span class="s" style="color: #d14;">'out_type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">splitName</span><span class="p">(</span><span class="n" style="color: #333;">db_file</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#644e37c5303095d9570d84c455cb6822d50aa50e"><strong>changeo.egg-info/PKG-INFO</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: changeo</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.0.<span class="idiff left right">0</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.0.<span class="idiff left right">1</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://changeo.readthedocs.io</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Namita Gupta, Jason Anthony Vander Heiden</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#fa6955e3d60d7ec84bad39b05425d008283df3bc"><strong>changeo.egg-info/SOURCES.txt</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">@@ -35,5 +35,4 @@ changeo/data/hh_s5f_dist.tsv</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">changeo/data/hs1f_compat_dist.tsv</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">changeo/data/m1n_compat_dist.tsv</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">changeo/data/mk_rs1nf_dist.tsv</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">changeo/data/mk_rs5nf_dist.tsv</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">changeo/data/receptor.tsv</span></pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">changeo/data/mk_rs5nf_dist.tsv</span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#1f4dd37096d2ddfcb225023d881d7065285142c4"><strong>changeo.egg-info/requires.txt</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">numpy>=1.8</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">scipy>=0.14</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">pandas>=0.24</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">biopython>=1.<span class="idiff left right">65</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">biopython>=1.<span class="idiff left right">71</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">PyYAML>=3.12</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">setuptools>=2.0</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">presto>=0.<span class="idiff left right">5.10</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">presto>=0.<span class="idiff left right">6.2</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">airr>=1.2.1</span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#05fdcdf376e61bb9ea4aa991f73cfd29b5aa07b3"><strong>changeo/IO.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">@@ -14,7 +14,6 @@ import zipfile</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="n" style="color: #333;">groupby</span><span class="p">,</span> <span class="n" style="color: #333;">zip_longest</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TemporaryDirectory</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Alphabet</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">IUPAC</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Presto and changeo imports</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1058,7 +1057,7 @@ class IgBLASTReader:</td>
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1058
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Reverse complement input sequence if required</span></span>
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'strand'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'-'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1061" class="line" lang="python"> <span class="n" style="color: #333;">seq_rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence_input'</span><span class="p">]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">IUPAC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ambiguous_dna</span></span><span class="p">).</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="python"> <span class="n" style="color: #333;">seq_rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence_input'</span><span class="p">]).</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence_input'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seq_rc</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'rev_comp'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'T'</span></span>
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#39d40dda335856b0a31785a995858f9160602e82"><strong>changeo/Version.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">@@ -5,5 +5,5 @@ Version and authorship information</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Namita Gupta, Jason Anthony Vander Heiden'</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Copyright 2020 Kleinstein Lab, Yale University. All rights reserved.'</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__license__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GNU Affero General Public License 3 (AGPL-3)'</span></span>
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<pre style="margin: 0;">-<span id="LC8" 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;">'1.0.<span class="idiff left right">0</span>'</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2020.<span class="idiff left right">05.06</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC8" 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;">'1.0.<span class="idiff left right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2020.<span class="idiff left right">10.13</span>'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#80b8baffe249ed1b18aa1e58fb5a921ea4e96247"><strong>changeo/data/receptor.tsv</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Name Type Description Change-O AIRR IMGT</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">sequence_id Unique sequence identifier identity SEQUENCE_ID sequence_id Sequence ID</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">sequence_input Query nucleotide sequence. nucleotide SEQUENCE_INPUT sequence Sequence</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">sequence_vdj Aligned V(D)J sequence. nucleotide SEQUENCE_VDJ ['V-D-J-REGION', 'V-J-REGION', 'V-REGION']</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">sequence_imgt IMGT-gapped, aligned V(D)J sequence. nucleotide SEQUENCE_IMGT sequence_alignment ['V-D-J-REGION', 'V-J-REGION', 'V-REGION']</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">junction Junction region nucleotide sequence. nucleotide JUNCTION junction JUNCTION</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">junction_aa Junction region amino acid sequence. aminoacid JUNCTION_AA junction_aa AA JUNCTION</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">junction_start Start position of the junction in the query sequence. integer JUNCTION start</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">junction_end End position of the junction in the query sequence. integer JUNCTION end</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">junction_length Number of nucleotides in the junction region. integer JUNCTION_LENGTH junction_length JUNCTION-nt nb</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">germline_vdj Inferred germline sequence aligned with the 'sequence_align' field. nucleotide GERMLINE_VDJ </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">germline_vdj_d_mask Inferred germline sequence aligned with the 'sequence_align' field and having the D segment masked. nucleotide GERMLINE_VDJ_D_MASK </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">germline_imgt Inferred germline sequence aligned with the 'sequence_imgt' field. nucleotide GERMLINE_IMGT germline_alignment </span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">germline_imgt_d_mask Inferred germline sequence aligned with the 'sequence_imgt' field and having the D segment masked. nucleotide GERMLINE_IMGT_D_MASK germline_alignment_d_mask </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">v_call V gene with allele. identity V_CALL v_call V-GENE and allele</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">d_call D gene with allele. identity D_CALL d_call D-GENE and allele</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">j_call J gene with allele. identity J_CALL j_call J-GENE and allele</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">c_call C region with allele. identity C_CALL c_call </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">locus Gene locus. identity LOCUS locus </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">rev_comp True if the the alignment is on the opposite strand (reverse complemented). boolean REV_COMP rev_comp Orientation</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">functional True if the V(D)J sequence is a functional gene and is predicted to be productive. boolean FUNCTIONAL productive V-DOMAIN Functionality</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">in_frame True if the V and J segment alignments are in-frame. boolean IN_FRAME vj_in_frame JUNCTION frame</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">stop True if the aligned sequence contains a stop codon. boolean STOP stop_codon V-DOMAIN Functionality comment</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">mutated_invariant True the aligment contains a mutated conserved amino acid. boolean MUTATED_INVARIANT mutated_invariant ['V-DOMAIN Functionality comment', 'V-REGION potential ins/del']</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">indels True if the V(D)J sequence contains insertions and/or deletions. boolean INDELS indels ['V-REGION potential ins/del', 'V-REGION insertions', 'V-REGION deletions']</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">v_seq_start Start position of the V segment in the query sequence. integer V_SEQ_START v_sequence_start V-REGION start</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">v_seq_end End of the V segment in the query sequence. integer v_sequence_end V-REGION end</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">v_seq_length Length of the V segment in the query sequence. integer V_SEQ_LENGTH </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">v_germ_start_vdj Alignment start position in the V reference sequence. integer V_GERM_START_VDJ </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">v_germ_end_vdj Alignment end position in the V reference sequence. integer </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">v_germ_length_vdj Alignment length in the V reference sequence. integer V_GERM_LENGTH_VDJ </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">v_germ_start_imgt Alignment start position in the IMGT-gapped V reference sequence. integer V_GERM_START_IMGT v_germline_start </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">v_germ_end_imgt Alignment end position in the IMGT-gapped V reference sequence. integer v_germline_end </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">v_germ_length_imgt Alignment length in the IMGT-gapped V reference sequence. integer V_GERM_LENGTH_IMGT </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">np1_start Start position of the nucleotides between the V and D segments or V and J segments. integer </span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">np1_end End position of the nucleotides between the V and D segments or V and J segments. integer </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">np1_length Number of nucleotides between the V and D segments or V and J segments. integer NP1_LENGTH np1_length "[""P3'V-nt nb"", 'N-REGION-nt nb', 'N1-REGION-nt nb', ""P5'D-nt nb""]"</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">d_seq_start Start position of the D segment in the query sequence. integer D_SEQ_START d_sequence_start D-REGION start</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">d_seq_end End position of the D segment in the query sequence. integer d_sequence_end D-REGION end</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">d_seq_length Length of the D segment in the query sequence. integer D_SEQ_LENGTH D-REGION-nt nb</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">d_germ_start Alignment start position in the D reference sequence. integer D_GERM_START d_germline_start 5'D-REGION trimmed-nt nb</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">d_germ_end Alignment end position in the D reference sequence. integer d_germline_end </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">d_germ_length Length of the alignment to the D reference sequence. integer D_GERM_LENGTH D-REGION-nt nb</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">np2_start Start position of the nucleotides between the D and J segments. integer </span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">np2_end End position of the nucleotides between the D and J segments. integer </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">np2_length Number of nucleotides between the D and J segments. integer NP2_LENGTH np2_length "[""P3'D-nt nb"", 'N2-REGION-nt nb', ""P5'J-nt nb""]"</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">j_seq_start Start position of the J segment in the query sequence. integer J_SEQ_START j_sequence_start J-REGION start</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">j_seq_end End position of the J segment in the query sequence. integer j_sequence_end J-REGION end</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">j_seq_length Length of the J segment in the query sequence. integer J_SEQ_LENGTH </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">j_germ_start Alignment start position in the J reference sequence. integer J_GERM_START j_germline_start 5'J-REGION trimmed-nt nb</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">j_germ_end Alignment start position in the J reference sequence. integer j_germline_end </span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">j_germ_length Alignment length of the J reference sequence. integer J_GERM_LENGTH </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">np1 Nucleotide sequence of the combined N/P region between the V and D segments or V and J segments. nucleotide NP1 np1 "[""P3'V"", 'N-REGION', 'N1-REGION', ""P5'D""]"</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">np2 Nucleotide sequence of the combined N/P region between the D and J segments. nucleotide NP2 np2 "[""P3'D"", 'N2-REGION', ""P5'J""]"</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">fwr1 Nucleotide sequence of the aligned FWR1 region. nucleotide FWR1_IMGT fwr1 FR1-IMGT</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">fwr2 Nucleotide sequence of the aligned FWR2 region. nucleotide FWR2_IMGT fwr2 FR2-IMGT</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">fwr3 Nucleotide sequence of the aligned FWR3 region. nucleotide FWR3_IMGT fwr3 FR3-IMGT</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">fwr4 Nucleotide sequence of the aligned FWR4 region. nucleotide FWR4_IMGT fwr4 FR4-IMGT</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">cdr1 Nucleotide sequence of the aligned CDR1 region. nucleotide CDR1_IMGT cdr1 CDR1-IMGT</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">cdr2 Nucleotide sequence of the aligned CDR2 region. nucleotide CDR2_IMGT cdr2 CDR2-IMGT</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">cdr3 Nucleotide sequence of the aligned CDR3 region. nucleotide CDR3_IMGT cdr3 CDR3-IMGT</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">fwr1_start FWR1 start position in the query sequence. integer fwr1_start FR1-IMGT start</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">fwr1_end FWR1 end position in the query sequence. integer fwr1_end FR1-IMGT end</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">fwr2_start FWR2 start position in the query sequence. integer fwr2_start FR2-IMGT start</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">fwr2_end FWR2 end position in the query sequence. integer fwr2_end FR2-IMGT end</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">fwr3_start FWR3 start position in the query sequence. integer fwr3_start FR3-IMGT start</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">fwr3_end FWR3 end position in the query sequence. integer fwr3_end FR3-IMGT end</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">fwr4_start FWR4 start position in the query sequence. integer fwr4_start FR4-IMGT start</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">fwr4_end FWR4 end position in the query sequence. integer fwr4_end FR4-IMGT end</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">cdr1_start CDR1 start position in the query sequence. integer cdr1_start CDR1-IMGT start</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">cdr1_end CDR1 end position in the query sequence. integer cdr1_end CDR1-IMGT end</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">cdr2_start CDR2 start position in the query sequence. integer cdr2_start CDR2-IMGT start</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">cdr2_end CDR2 end position in the query sequence. integer cdr2_end CDR2-IMGT end</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">cdr3_start CDR3 start position in the query sequence. integer cdr3_start CDR3-IMGT start</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">cdr3_end CDR3 end position in the query sequence. integer cdr3_end CDR3-IMGT end</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">v_score V alignment score. float V_SCORE v_score V-REGION score</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">v_identity V alignment fractional identity. float V_IDENTITY v_identity V-REGION identity %</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">v_evalue V alignment E-value. float V_EVALUE v_support </span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">v_cigar V alignment CIGAR string. identity V_CIGAR v_cigar </span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">v_btop V alignment BTOP string. identity V_BTOP </span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">d_score D alignment score. float D_SCORE d_score D-REGION score</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">d_identity D alignment fractional identity. float D_IDENTITY d_identity D-REGION identity %</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">d_evalue D alignment E-value. float D_EVALUE d_support </span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">d_cigar D alignment CIGAR string. identity D_CIGAR d_cigar </span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">d_btop D alignment BTOP string. identity D_BTOP </span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">j_score J alignment score. float J_SCORE j_score J-REGION score</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">j_identity J alignment fractional identity. float J_IDENTITY j_identity J-REGION identity %</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">j_evalue J alignment E-value. float J_EVALUE j_support </span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">j_cigar J alignment CIGAR string. identity J_CIGAR j_cigar </span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">j_btop V alignment BTOP string. identity J_BTOP </span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">c_score C region alignment score. float C_SCORE c_score </span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">c_identity C region alignment fractional identity. float C_IDENTITY c_identity </span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">c_evalue C region alignment E-value. float C_EVALUE c_support </span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">c_cigar C region alignment CIGAR string. identity C_CIGAR c_cigar </span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">c_btop V alignment BTOP string. identity C_BTOP </span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">vdj_score Alignment score for aligners that consider the full sequence. float VDJ_SCORE vdj_score </span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">vdj_identity Alignment fractional identity for aligners that consider the full sequence. float VDJ_IDENTITY vdj_identity </span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">vdj_evalue Alignment E-value for aligners that consider the full sequence. float VDJ_EVALUE vdj_support </span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">vdj_cigar CIGAR string for the full V(D)J alignment. identity VDJ_CIGAR vdj_cigar </span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext">vdj_btop BTOP string for the full V(D)J alignment. identity VDJ_BTOP </span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">n1_length Number of untemplated nucleotides 5' of the D segment. integer N1_LENGTH n1_length ['N-REGION-nt nb', 'N1-REGION-nt nb']</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">n2_length Number of untemplated nucleotides 3' of the D segment. integer N2_LENGTH n2_length N2-REGION-nt nb</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">p3v_length Number of palindromic nucleotides 3' of the V segment. integer P3V_LENGTH p3v_length P3'V-nt nb</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext">p5d_length Number of palindromic nucleotides 5' of the D segment. integer P5D_LENGTH p5d_length P5'D-nt nb</span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">p3d_length Number of palindromic nucleotides 3' of the D segment. integer P3D_LENGTH p3d_length P3'D-nt nb</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">p5j_length Number of palindromic nucleotides 5' of the J segment. integer P5J_LENGTH p5j_length P5'J-nt nb</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">d_frame Reading frame of the D segment. integer D_FRAME D-REGION reading frame</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">dupcount Copy number or number of duplicate observations of the sequence. integer DUPCOUNT duplicate_count </span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">conscount Number of reads contributing to the (UMI) consensus for this sequence. integer CONSCOUNT consensus_count </span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">clone Clonal cluster assignment for the query sequence. identity CLONE clone_id </span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">cell Cell identifier. identity CELL cell_id </span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/fc08a33fe0fc1638ea20e03e42a849994955b825#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/numpy" rel="nofollow noreferrer noopener" target="_blank">numpy</a>>=1.8</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/scipy" rel="nofollow noreferrer noopener" target="_blank">scipy</a>>=0.14</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pandas" rel="nofollow noreferrer noopener" target="_blank">pandas</a>>=0.24</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biopython" rel="nofollow noreferrer noopener" target="_blank">biopython</a>>=1.<span class="idiff left right">65</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/biopython" rel="nofollow noreferrer noopener" target="_blank">biopython</a>>=1.<span class="idiff left right">71</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/PyYAML" rel="nofollow noreferrer noopener" target="_blank">PyYAML</a>>=3.12</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/setuptools" rel="nofollow noreferrer noopener" target="_blank">setuptools</a>>=2.0</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/presto" rel="nofollow noreferrer noopener" target="_blank">presto</a>>=0.<span class="idiff left right">5.10</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/presto" rel="nofollow noreferrer noopener" target="_blank">presto</a>>=0.<span class="idiff left right">6.2</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/airr" rel="nofollow noreferrer noopener" target="_blank">airr</a>>=1.2.1</span></pre>
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