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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/changeo">Debian Med / changeo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/changeo/-/commit/46594f9a8c6088af6003a1cb0205d0f6b2cc5970">46594f9a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-09T23:08:07+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/changeo/-/commit/05bc29b86f5759d374734a81ecbd4e11ea327f58">05bc29b8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-09T23:08:07+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/tests/run-unit-tests: Change checksums in output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/changeo/-/commit/1215c9170cffeaebdd365f6fd3fa3962f288c89d">1215c917</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-09T23:08:07+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
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<h4>15 changed files:</h4>
<ul>
<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="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#d695b01121955eec5b7bf60e65e337feb246adfc">
bin/MakeDb.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="#1f4dd37096d2ddfcb225023d881d7065285142c4">
changeo.egg-info/requires.txt
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<li class="file-stats">
<a href="#026f0d97c5b3ab8c201d9113701cd143c506d485">
changeo/Commandline.py
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<li class="file-stats">
<a href="#25c988bb25af0090dbaf6b9dab25ea8d705dd5b7">
changeo/Defaults.py
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<li class="file-stats">
<a href="#b5069239871a460c62282af610b741a1c59789b1">
changeo/Gene.py
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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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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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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/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#3374c1c18de688d968548dc001e40ee700f04f6f"><strong>INSTALL.rst</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,9 +23,9 @@ The minimum dependencies for installation are:</td>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="old_line diff-line-num" data-linenumber="24" 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="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">+ `SciPy 0.14 <http://scipy.org>`__</span>
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<td class="old_line diff-line-num" data-linenumber="25" 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="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">+ `pandas 0.24 <http://pandas.pydata.org>`__</span>
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<td class="old_line diff-line-num old" data-linenumber="26" 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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<td class="new_line diff-line-num old" data-linenumber="26" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">+ `Biopython 1.7<span class="idiff left right">1</span> <http://biopython.org>`__</span>
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<td class="old_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="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">
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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="LC26" class="line" lang="plaintext">+ `Biopython 1.7<span class="idiff left right">7</span> <http://biopython.org>`__</span>
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<td class="old_line diff-line-num" data-linenumber="27" 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="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">+ `presto 0.6.2 <http://presto.readthedocs.io>`__</span>
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<td class="old_line diff-line-num old" data-linenumber="28" 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="LC28" class="line" lang="plaintext">+ `airr 1.<span class="idiff left right">2</span>.1 <https://docs.airr-community.org>`__</span>
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<td class="old_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="28" 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="LC28" class="line" lang="plaintext">+ `airr 1.<span class="idiff left right">3</span>.1 <https://docs.airr-community.org>`__</span>
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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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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<td class="old_line diff-line-num" data-linenumber="31" 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="LC31" class="line" lang="plaintext">Those tools require minimum versions of:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="45" 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">@@ -45,7 +45,7 @@ Linux</td>
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<td class="new_line diff-line-num" data-linenumber="45" 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="LC45" class="line" lang="plaintext"> Biopython according to its</span>
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<td class="old_line diff-line-num" data-linenumber="46" 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="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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<td class="old_line diff-line-num old" data-linenumber="48" 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="LC48" class="line" lang="plaintext">2. Install `presto 0.<span class="idiff left right">5.10</span> <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.<span class="idiff left right">6.2</span> <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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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,7 +86,7 @@ Mac OS X</td>
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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="LC89" class="line" lang="plaintext">8. Install `presto 0.<span class="idiff left right">5.10</span> <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.<span class="idiff left right">6.2</span> <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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,7 +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="LC107" class="line" lang="plaintext">3. Install `presto 0.<span class="idiff left right">5.10</span> <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.<span class="idiff left right">6.2</span> <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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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#8e9983d68bc118797b12e3c989281a14e4ae4a62"><strong>NEWS.rst</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Release Notes</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">===============================================================================</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Version 1.1.0: June 21, 2021</span>
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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"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">+ Fixed gene parsing for IMGT temporary designation nomenclature.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">+ Updated dependencies to biopython >= v1.77, airr >= v1.3.1, PyYAML>=5.1.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">MakeDb:</span>
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11
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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">+ Added the ``--imgt-id-len`` argument to accommodate changes introduced in how</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> IMGT/HighV-QUEST truncates sequence identifiers as of version 1.8.3 (May 7, 2021).</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> The header lines in the fasta files are now truncated to 49 characters. In</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> IMGT/HighV-QUEST versions older that 1.8.3, they were truncated to 50 characters.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ``--imgt-id-len`` default value is 49. Users should specify ``--imgt-id-len 50``</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> to analyze IMGT results generated with IMGT/HighV-QUEST versions older that 1.8.3.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">+ Added the ``--infer-junction`` argument to ``MakeDb igblast``, to enable the inference</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> of the junction sequence when not reported by IgBLAST. Should be used with data from</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> IgBLAST v1.6.0 or older; before igblast added the IMGT-CDR3 inference.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Version 1.0.2: January 18, 2021</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">-------------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">AlignRecords:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">+ Fixed a bug caused the program to exit when encountering missing sequence</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">data. It will now fail the row or group with missing data and continue.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"><span class="idiff left right"> </span>data. It will now fail the row or group with missing data and continue.</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">MakeDb:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,7 +88,7 @@ MakeDb:</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">+ Add --regions argument to the ``igblast`` and ``igblast-aa`` subcommands</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> to allow specification of the IMGT CDR/FWR region boundaries. Currently,</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> the supported specifications are ``default`` (human, mouse) and</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> <span class="idiff left right"> </span>``rhesus-igl``.</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> ``rhesus-igl``.</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">Version 0.4.6: July 19, 2019</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#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.<span class="idiff left right">0.2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.<span class="idiff left right">1.0</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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: immcantation@googlegroups.com</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: GNU Affero General Public License 3 (AGPL-3)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Download-URL: https://bitbucket.org/kleinstein/changeo/downloads</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Description: Change-O - Repertoire clonal assignment toolkit</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Description: .. image:: https://img.shields.io/pypi/dm/changeo</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> :target: https://pypi.org/project/changeo</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> .. image:: https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> :target: https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Change-O - Repertoire clonal assignment toolkit</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> ================================================================================</span>
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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"> Change-O is a collection of tools for processing the output of V(D)J alignment</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. image:: https://img.shields.io/pypi/dm/changeo</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> :target: https://pypi.org/project/changeo</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.. image:: https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> :target: https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html</span>
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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">Change-O - Repertoire clonal assignment toolkit</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">================================================================================</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#d695b01121955eec5b7bf60e65e337feb246adfc"><strong>bin/MakeDb.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 +20,7 @@ from Bio import SeqIO</td>
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<pre style="margin: 0;"> <span id="LC20" 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="LC21" 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;">parseAnnotation</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;">presto.IO</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">countSeqFile</span><span class="p">,</span> <span class="n" style="color: #333;">printLog</span><span class="p">,</span> <span class="n" style="color: #333;">printMessage</span><span class="p">,</span> <span class="n" style="color: #333;">printProgress</span><span class="p">,</span> <span class="n" style="color: #333;">printError</span><span class="p">,</span> <span class="n" style="color: #333;">printWarning</span><span class="p">,</span> <span class="n" style="color: #333;">readSeqFile</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;">changeo.Defaults</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">default_format</span><span class="p">,</span> <span class="n" style="color: #333;">default_out_args</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;">changeo.Defaults</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">default_format</span><span class="p">,</span> <span class="n" style="color: #333;">default_out_args</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">default_imgt_id_len</span></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">changeo.Commandline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CommonHelpFormatter</span><span class="p">,</span> <span class="n" style="color: #333;">checkArgs</span><span class="p">,</span> <span class="n" style="color: #333;">getCommonArgParser</span><span class="p">,</span> <span class="n" style="color: #333;">parseCommonArgs</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;">changeo.Alignment</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RegionDefinition</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">changeo.Gene</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">buildGermline</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" 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">@@ -102,7 +102,7 @@ def addGermline(receptor, references, amino_acid=False):</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">receptor</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getIDforIMGT</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getIDforIMGT</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">imgt_id_len</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">default_imgt_id_len</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> Create a sequence ID translation using IMGT truncation.</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,13 +113,13 @@ def getIDforIMGT(seq_file):</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> dict : a dictionary of with the IMGT truncated ID as the key and the full sequence description as the value.</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create a sequence ID translation using IDs truncate up to space or <span class="idiff left right">50</span> chars</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create a sequence ID translation using IDs truncate up to space or <span class="idiff left right">49</span> chars</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">readSeqFile</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;"><span class="idiff left right">50</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;"><span class="idiff left right">imgt_id_len</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">id_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">description</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">id_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">'\||\s|!|&|\*|<|>|\?'</span><span class="p">,</span> <span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">[:</span><span class="mi" style="color: #099;"><span class="idiff left right">50</span></span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">id_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">'\||\s|!|&|\*|<|>|\?'</span><span class="p">,</span> <span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">[:</span><span class="n" style="color: #333;"><span class="idiff left right">imgt_id_len</span></span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">ids</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="n" style="color: #333;">id_key</span><span class="p">:</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ids</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">@@ -355,7 +355,7 @@ def writeDb(records, fields, aligner_file, total_count, id_dict=None, annotation</td>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parseIMGT</span><span class="p">(</span><span class="n" style="color: #333;">aligner_file</span><span class="p">,</span> <span class="n" style="color: #333;">seq_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">repo</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">cellranger_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">partial</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">asis_id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">extended</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_format</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">out_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_out_args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">extended</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_format</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">out_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_out_args</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">imgt_id_len</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">default_imgt_id_len</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"><span class="s" style="color: #d14;"> Main for IMGT aligned sample sequences.</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="369" 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="369" 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">@@ -369,6 +369,7 @@ def parseIMGT(aligner_file, seq_file=None, repo=None, cellranger_file=None, part</td>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"><span class="s" style="color: #d14;"> format : output format. one of 'changeo' or 'airr'.</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"><span class="s" style="color: #d14;"> out_file : output file name. Automatically generated from the input file if None.</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"><span class="s" style="color: #d14;"> out_args : common output argument dictionary from parseCommonArgs.</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"><span class="s" style="color: #d14;"> imgt_id_len: maximum character length of sequence identifiers reported by IMGT/HighV-QUEST.</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"><span class="s" style="color: #d14;"> dict : names of the 'pass' and 'fail' output files.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="394" 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="395" 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">@@ -394,8 +395,8 @@ def parseIMGT(aligner_file, seq_file=None, repo=None, cellranger_file=None, part</td>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">total_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countDbFile</span><span class="p">(</span><span class="n" style="color: #333;">imgt_files</span><span class="p">[</span><span class="s" style="color: #d14;">'summary'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get (parsed) IDs from fasta file submitted to IMGT</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">id_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getIDforIMGT</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_file</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">id_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getIDforIMGT</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">imgt_id_len</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_file</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Load supplementary annotation table</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cellranger_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cellranger_extended</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extended</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cellranger_base</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="437" 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">@@ -436,7 +437,6 @@ def parseIMGT(aligner_file, seq_file=None, repo=None, cellranger_file=None, part</td>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="s" style="color: #d14;">'...'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">references</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()):</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">'Germline reference sequences do not appear to contain IMGT-numbering spacers. Results may be incorrect.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">germ_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">addGermline</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parse_iter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write db</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeDb</span><span class="p">(</span><span class="n" style="color: #333;">germ_iter</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fields</span><span class="p">,</span> <span class="n" style="color: #333;">aligner_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">aligner_file</span><span class="p">,</span> <span class="n" style="color: #333;">total_count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_count</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">annotations</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">annotations</span><span class="p">,</span> <span class="n" style="color: #333;">id_dict</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">id_dict</span><span class="p">,</span> <span class="n" style="color: #333;">asis_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">asis_id</span><span class="p">,</span> <span class="n" style="color: #333;">partial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">partial</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">@@ -449,7 +449,7 @@ def parseIMGT(aligner_file, seq_file=None, repo=None, cellranger_file=None, part</td>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parseIgBLAST</span><span class="p">(</span><span class="n" style="color: #333;">aligner_file</span><span class="p">,</span> <span class="n" style="color: #333;">seq_file</span><span class="p">,</span> <span class="n" style="color: #333;">repo</span><span class="p">,</span> <span class="n" style="color: #333;">amino_acid</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">cellranger_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">partial</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">asis_id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">asis_calls</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">extended</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">asis_id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">asis_calls</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">extended</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">infer_junction</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'changeo'</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">out_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_out_args</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"><span class="s" style="color: #d14;"> Main for IgBLAST aligned sample sequences.</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">@@ -464,6 +464,7 @@ def parseIgBLAST(aligner_file, seq_file, repo, amino_acid=False, cellranger_file</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"><span class="s" style="color: #d14;"> asis_calls (bool): if True do not parse gene calls for allele names.</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"><span class="s" style="color: #d14;"> extended (bool): if True add alignment scores, FWR regions, and CDR regions to the output.</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"><span class="s" style="color: #d14;"> regions (str): name of the IMGT FWR/CDR region definitions to use.</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"><span class="s" style="color: #d14;"> infer_junction (bool): if True, infer the junction sequence, if not reported by IgBLAST.</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"><span class="s" style="color: #d14;"> format (str): output format. one of 'changeo' or 'airr'.</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python"><span class="s" style="color: #d14;"> out_file (str): output file name. Automatically generated from the input file if None.</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"><span class="s" style="color: #d14;"> out_args (dict): common output argument dictionary from parseCommonArgs.</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">@@ -481,6 +482,7 @@ def parseIgBLAST(aligner_file, seq_file, repo, amino_acid=False, cellranger_file</td>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'ASIS_CALLS'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">asis_calls</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'PARTIAL'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partial</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'EXTENDED'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extended</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'INFER_JUNCTION'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infer_junction</span></span>
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<pre style="margin: 0;"> <span id="LC486" 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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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set amino acid conditions</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">@@ -531,7 +533,7 @@ def parseIgBLAST(aligner_file, seq_file, repo, amino_acid=False, cellranger_file</td>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse and write output</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">aligner_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">parse_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">regions</span><span class="p">,</span> <span class="n" style="color: #333;">asis_calls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">asis_calls</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333;">parse_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">regions</span><span class="p">,</span> <span class="n" style="color: #333;">asis_calls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">asis_calls</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">infer_junction</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">infer_junction</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">germ_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">addGermline</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">amino_acid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">amino_acid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parse_iter</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeDb</span><span class="p">(</span><span class="n" style="color: #333;">germ_iter</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fields</span><span class="p">,</span> <span class="n" style="color: #333;">aligner_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">aligner_file</span><span class="p">,</span> <span class="n" style="color: #333;">total_count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">total_count</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">annotations</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">annotations</span><span class="p">,</span> <span class="n" style="color: #333;">amino_acid</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">amino_acid</span><span class="p">,</span> <span class="n" style="color: #333;">partial</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">partial</span><span class="p">,</span> <span class="n" style="color: #333;">asis_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">asis_id</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">@@ -724,6 +726,9 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--regions'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'regions'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rhesus-igl'</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''IMGT CDR and FWR boundary definition to use.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--infer-junction'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'infer_junction'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''Infer the junction sequence. For use with IgBLAST v1.6.0 or older, </span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python"><span class="s" style="color: #d14;"> prior to the addition of IMGT-CDR3 inference.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="python"> <span class="n" style="color: #333;">parser_igblast</span><span class="p">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseIgBLAST</span><span class="p">,</span> <span class="n" style="color: #333;">amino_acid</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># igblastp output parser</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">@@ -809,6 +814,11 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"><span class="s" style="color: #d14;"> Adds <vdj>_score, <vdj>_identity>, fwr1, fwr2, fwr3, fwr4,</span></span>
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"><span class="s" style="color: #d14;"> cdr1, cdr2, cdr3, n1_length, n2_length, p3v_length, p5d_length, </span></span>
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="python"><span class="s" style="color: #d14;"> p3d_length, p5j_length and d_frame.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="python"> <span class="n" style="color: #333;">group_imgt</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--imgt-id-len'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'imgt_id_len'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_imgt_id_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''The maximum character length of sequence identifiers reported by IMGT/HighV-QUEST. </span></span>
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"><span class="s" style="color: #d14;"> Specify 50 if the IMGT files (-i) were generated with an IMGT/HighV-QUEST version older </span></span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="python"><span class="s" style="color: #d14;"> than 1.8.3 (May 7, 2021).'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"> <span class="n" style="color: #333;">parser_imgt</span><span class="p">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parseIMGT</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># iHMMuneAlign Aligner</span></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#644e37c5303095d9570d84c455cb6822d50aa50e"><strong>changeo.egg-info/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.<span class="idiff left right">0.2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.<span class="idiff left right">1.0</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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: immcantation@googlegroups.com</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: GNU Affero General Public License 3 (AGPL-3)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Download-URL: https://bitbucket.org/kleinstein/changeo/downloads</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Description: Change-O - Repertoire clonal assignment toolkit</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Description: .. image:: https://img.shields.io/pypi/dm/changeo</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> :target: https://pypi.org/project/changeo</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> .. image:: https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> :target: https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Change-O - Repertoire clonal assignment toolkit</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> ================================================================================</span>
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12
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> </span>
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13
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> Change-O is a collection of tools for processing the output of V(D)J alignment</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#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>=1.7<span class="idiff left right">1</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">PyYAML>=<span class="idiff left">3</span>.1<span class="idiff right">2</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">biopython>=1.7<span class="idiff left right">7</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">PyYAML>=<span class="idiff left right">5</span>.1</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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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">presto>=0.6.2</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">airr>=1.<span class="idiff left right">2</span>.1</span></pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">airr>=1.<span class="idiff left right">3</span>.1</span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#026f0d97c5b3ab8c201d9113701cd143c506d485"><strong>changeo/Commandline.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">@@ -110,8 +110,10 @@ def getCommonArgParser(db_in=True, db_out=True, out_file=True, failed=True, log=</td>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> fail processing.'''</span><span class="p">)</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Format arguments</span></span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">format</span><span class="p">:</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'format'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_format</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">choices_format</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''Specify input and output format.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'format'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_format</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">choices_format</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''Output format. Also specifies the input format for tools accepting </span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> tab delimited AIRR Rearrangement or Change-O files.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Multiprocessing arguments</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multiproc</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#25c988bb25af0090dbaf6b9dab25ea8d705dd5b7"><strong>changeo/Defaults.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">@@ -42,3 +42,6 @@ default_out_args = {'log_file': None,</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'out_name'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'out_type'</span><span class="p">:</span> <span class="s" style="color: #d14;">'tsv'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">'failed'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># IMGT</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">default_imgt_id_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">49</span></span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#b5069239871a460c62282af610b741a1c59789b1"><strong>changeo/Gene.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">@@ -14,14 +14,14 @@ from changeo.Defaults import v_attr, d_attr, j_attr, seq_attr</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Ig and TCR Regular expressions</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">allele_number_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'(?<=\*)([\.\w]+)'</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])([VDJ][A-<span class="idiff left right">Z</span>0-9]+[-/\w]*[-\*][\.\w]+))'</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">gene_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])([VDJ][A-<span class="idiff left right">Z</span>0-9]+[-/\w]*))'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">family_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])([VDJ][A-<span class="idiff left right">Z</span>0-9]+))'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])([VDJ][A-<span class="idiff left right">R</span>0-9]+[-/\w]*[-\*][\.\w]+))'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">gene_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])([VDJ][A-<span class="idiff left right">R</span>0-9]+[-/\w]*))'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">family_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])([VDJ][A-<span class="idiff left right">R</span>0-9]+))'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="n" style="color: #333;">locus_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'(IG[HLK]|TR[ABGD])'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">v_allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])V[A-<span class="idiff left right">Z</span>0-9]+[-/\w]*[-\*][\.\w]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">d_allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])D[A-<span class="idiff left right">Z</span>0-9]+[-/\w]*[-\*][\.\w]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">j_allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])J[A-<span class="idiff left right">Z</span>0-9]+[-/\w]*[-\*][\.\w]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">v_allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])V[A-<span class="idiff left right">R</span>0-9]+[-/\w]*[-\*][\.\w]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">d_allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])D[A-<span class="idiff left right">R</span>0-9]+[-/\w]*[-\*][\.\w]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">j_allele_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])J[A-<span class="idiff left right">R</span>0-9]+[-/\w]*[-\*][\.\w]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">c_gene_regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'((IG[HLK]|TR[ABGD])([DMAGEC][P0-9]?[A-Z]?))'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -883,7 +883,8 @@ class IgBLASTReader:</td>
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fields</span></span>
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">igblast</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">asis_calls</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span> <span class="n" style="color: #333;">receptor</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">igblast</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">asis_calls</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'default'</span><span class="p">,</span> <span class="n" style="color: #333;">receptor</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="python"> <span class="n" style="color: #333;">infer_junction</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="python"><span class="s" style="color: #d14;"> Initializer.</span></span>
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -895,6 +896,7 @@ class IgBLASTReader:</td>
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="python"><span class="s" style="color: #d14;"> asis_calls (bool): if True do not parse gene calls for allele names.</span></span>
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="python"><span class="s" style="color: #d14;"> regions (str): name of the IMGT FWR/CDR region definitions to use.</span></span>
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="python"><span class="s" style="color: #d14;"> receptor (bool): if True (default) iteration returns an Receptor object, otherwise it returns a dictionary.</span></span>
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="python"><span class="s" style="color: #d14;"> infer_junction (bool): if True, infer the junction region if not reported by IgBLAST.</span></span>
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="python"><span class="s" style="color: #d14;"> changeo.IO.IgBLASTReader</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">@@ -906,6 +908,7 @@ class IgBLASTReader:</td>
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">regions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">regions</span></span>
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">asis_calls</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">asis_calls</span></span>
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">receptor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">receptor</span></span>
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">infer_junction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infer_junction</span></span>
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define parsing blocks</span></span>
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">igblast</span><span class="p">,</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="s" style="color: #d14;">'# IGBLAST'</span><span class="p">,</span> <span class="n" style="color: #333;">x</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">@@ -1472,7 +1475,7 @@ class IgBLASTReader:</td>
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'subregion'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sections</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'cdr3_igblast_start'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sections</span><span class="p">[</span><span class="s" style="color: #d14;">'subregion'</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC1476" class="line" lang="python"> <span class="n" style="color: #333;">junc_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parseSubregionSection</span><span class="p">(</span><span class="n" style="color: #333;">sections</span><span class="p">[</span><span class="s" style="color: #d14;">'subregion'</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>
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<pre style="margin: 0;"> <span id="LC1477" class="line" lang="python"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">junc_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1475" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="s" style="color: #d14;">'j_call'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'j_call'</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">'sequence_imgt'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence_imgt'</span><span class="p">]):</span></span>
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<pre style="margin: 0;">+<span id="LC1478" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">infer_junction</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff right"> </span><span class="p">(</span><span class="s" style="color: #d14;">'j_call'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'j_call'</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">'sequence_imgt'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence_imgt'</span><span class="p">]):</span></span>
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="python"> <span class="n" style="color: #333;">junc_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inferJunction</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence_imgt'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC1480" class="line" lang="python"> <span class="n" style="color: #333;">j_germ_start</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'j_germ_start'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="python"> <span class="n" style="color: #333;">j_germ_length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db</span><span class="p">[</span><span class="s" style="color: #d14;">'j_germ_length'</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">@@ -2474,4 +2477,4 @@ def yamlDict(file):</td>
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<pre style="margin: 0;"> <span id="LC2477" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC2478" class="line" lang="python"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">'YAML file is invalid.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2479" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC2477" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">yaml_dict</span></span></pre>
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<pre style="margin: 0;">+<span id="LC2480" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">yaml_dict</span></span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#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">@@ -3,7 +3,7 @@ Version and authorship information</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__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 202<span class="idiff left right">1</span> 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.<span class="idiff left right">0.2</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;">'2021.0<span class="idiff left right">1.18</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.<span class="idiff left right">1.0</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;">'2021.0<span class="idiff left right">6.21</span>'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">changeo (1.1.0-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 1.1.0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * d/tests/run-unit-tests: Change checksums in output</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Fri, 09 Jul 2021 23:07:44 +0530</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">changeo (1.0.2-2~0exp0) experimental; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,13 +16,13 @@ gunzip -r *</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell">MakeDb.py imgt <span class="nt" style="color: #000080;">-i</span> S43_atleast-2.txz <span class="nt" style="color: #000080;">-s</span> S43_atleast-2.fasta</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">025d331569cf3959735d1677ad1532d9</span> S43_atleast-2_db-pass.tsv"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">fca65a99ea3569b99196c50c42269946</span> S43_atleast-2_db-pass.tsv"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell">CreateGermlines.py <span class="nt" style="color: #000080;">-d</span> S43_atleast-2_db-pass.tsv <span class="nt" style="color: #000080;">-g</span> dmask <span class="nt" style="color: #000080;">-r</span> IMGT_Human_IGHV.fasta IMGT_Human_IGHD.fasta IMGT_Human_IGHJ.fasta</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"8<span class="idiff left right">a5a1673f5a3e566a0c2a901bdf2a278</span> S43_atleast-2_db-pass_germ-pass.tsv"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"8<span class="idiff left right">b76920fd30d640d34af22009621cc2e</span> S43_atleast-2_db-pass_germ-pass.tsv"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell">ParseDb.py <span class="k" style="font-weight: 600;">select</span> <span class="nt" style="color: #000080;">-d</span> S43_atleast-2_db-pass.tsv <span class="nt" style="color: #000080;">-f</span> productive <span class="nt" style="color: #000080;">-u</span> T</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">23ae15ac46bc1d83cfa9e615e8af3703</span> S43_atleast-2_db-pass_parse-select.tsv"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">7cf6dffe3d45414021d214da9ad6dc1e</span> S43_atleast-2_db-pass_parse-select.tsv"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums</span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/compare/908fd41c08bc8d600e1c082a3b1f4ac4ea5f0a67...1215c9170cffeaebdd365f6fd3fa3962f288c89d#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>>=1.7<span class="idiff left right">1</span></span>
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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>>=<span class="idiff left">3</span>.1<span class="idiff right">2</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>>=1.7<span class="idiff left right">7</span></span>
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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>>=<span class="idiff left right">5</span>.1</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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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>>=0.6.2</span>
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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.<span class="idiff left right">2</span>.1</span></pre>
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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.<span class="idiff left right">3</span>.1</span></pre>
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