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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/changeo">Debian Med / changeo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446">da695a88</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-11-01T23:47:16+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.0</pre>
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<h4>12 changed files:</h4>
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<li class="file-stats">
<a href="#3374c1c18de688d968548dc001e40ee700f04f6f">
INSTALL.rst
</a>
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<li class="file-stats">
<a href="#8e9983d68bc118797b12e3c989281a14e4ae4a62">
NEWS.rst
</a>
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<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#4db8b1dde66a1a0c949dfe6e2bfb229fb253d1ba">
bin/AssignGenes.py
</a>
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<li class="file-stats">
<a href="#9e737285d616e5329acd417dcc52901d591b83d8">
bin/BuildTrees.py
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<li class="file-stats">
<a href="#d695b01121955eec5b7bf60e65e337feb246adfc">
bin/MakeDb.py
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<li class="file-stats">
<a href="#b07d9f16b53c7bf45411d329e0d2defdd381c644">
bin/ParseDb.py
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<li class="file-stats">
<a href="#644e37c5303095d9570d84c455cb6822d50aa50e">
changeo.egg-info/PKG-INFO
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<li class="file-stats">
<a href="#1f4dd37096d2ddfcb225023d881d7065285142c4">
changeo.egg-info/requires.txt
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<li class="file-stats">
<a href="#05fdcdf376e61bb9ea4aa991f73cfd29b5aa07b3">
changeo/IO.py
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<li class="file-stats">
<a href="#39d40dda335856b0a31785a995858f9160602e82">
changeo/Version.py
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<h4>Changes:</h4>
<li id="3374c1c18de688d968548dc001e40ee700f04f6f">
<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#3374c1c18de688d968548dc001e40ee700f04f6f"><strong>INSTALL.rst</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ The minimum dependencies for installation are:</td>
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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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<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" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">+ `Biopython 1.77 <http://biopython.org>`__</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="27" 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="27" 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="LC27" class="line" lang="plaintext">+ `presto 0.<span class="idiff left right">6.2</span> <http://presto.readthedocs.io>`__</span>
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<td class="old_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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<td class="new_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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">+ `presto 0.<span class="idiff left right">7.0</span> <http://presto.readthedocs.io>`__</span>
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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">+ `airr 1.3.1 <https://docs.airr-community.org>`__</span>
</pre>
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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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<td class="new_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="30" 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="30" 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="LC30" class="line" lang="plaintext">Some tools wrap external applications that are not required for installation.</span>
</pre>
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<li id="8e9983d68bc118797b12e3c989281a14e4ae4a62">
<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#8e9983d68bc118797b12e3c989281a14e4ae4a62"><strong>NEWS.rst</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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 1.2.0: October 29, 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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<td class="new_line diff-line-num new" data-linenumber="7" 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="LC7" class="line" lang="plaintext">+ Updated dependencies to presto >= v0.7.0.</span>
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<td class="old_line diff-line-num new" data-linenumber="4" 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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">AssignGenes:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">+ Fixed reporting of IgBLAST output counts when specifying ``--format airr``.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">BuildTrees:</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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">+ Added support for specifying fixed omega and hotness parameters at the</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> commandline.</span>
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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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">CreateGermlines:</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">+ Will now use the first allele in the reference database when duplicate</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> allele names are provided. Only appears to affect mouse BCR light chains</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> and TCR alleles in the IMGT database when the same allele name differs by</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> strain.</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">MakeDb:</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">+ Added support for changes in how IMGT/HighV-QUEST v1.8.4 handles special</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> characters in sequence identifiers.</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">+ Fixed the ``imgt`` subcommand incorrectly allowing execution without</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> specifying the IMGT/HighV-QUEST output file at the commandline.</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">ParseDb:</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">+ Added reporting of output file sizes to the console log of the ``split``</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> subcommand.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Version 1.1.0: June 21, 2021</span>
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5
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<pre style="margin: 0;"> <span id="LC39" 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">@@ -8,13 +42,12 @@ Version 1.1.0: June 21, 2021</td>
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<pre style="margin: 0;"> <span id="LC42" 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="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">MakeDb:</span>
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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="LC45" 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 v<span class="idiff left right">ersion </span>1.8.3 (May 7, 2021).</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> IMGT/HighV-QUEST truncates sequence identifiers as of v1.8.3 (May 7, 2021).</span>
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<pre style="margin: 0;"> <span id="LC47" 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 tha<span class="idiff left right">t </span>1.8.3, they were truncated to 50 characters.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> IMGT/HighV-QUEST versions older tha<span class="idiff left right">n v</span>1.8.3, they were truncated to 50 characters.</span>
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<pre style="margin: 0;"> <span id="LC49" 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 tha<span class="idiff left right">t </span>1.8.3.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> to analyze IMGT results generated with IMGT/HighV-QUEST versions older tha<span class="idiff left right">n v</span>1.8.3.</span>
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<pre style="margin: 0;"> <span id="LC51" 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="LC52" 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="LC53" 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="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">1</span>.0</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.<span class="idiff left right">2</span>.0</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://changeo.readthedocs.io</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Namita Gupta, Jason Anthony Vander Heiden</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#4db8b1dde66a1a0c949dfe6e2bfb229fb253d1ba"><strong>bin/AssignGenes.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">@@ -14,6 +14,7 @@ from collections import OrderedDict</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pkg_resources</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parse_version</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">textwrap</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dedent</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">time</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">time</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Presto imports</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">presto.IO</span> <span class="kn" style="font-weight: 600;">import</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;">printError</span><span class="p">,</span> <span class="n" style="color: #333;">printWarning</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">@@ -99,9 +100,30 @@ def assignIgBLAST(seq_file, amino_acid=False, igdata=default_igdata, loci='ig',</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">vdb</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">vdb</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nproc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">exec</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">igblast_exec</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">printMessage</span><span class="p">(</span><span class="s" style="color: #d14;">'Done'</span><span class="p">,</span> <span class="n" style="color: #333;">start_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start_time</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">25</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get number of processed sequences</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'blast'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC106" 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;">out_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">SEEK_END</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">SEEK_CUR</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">pass_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">().</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">num_seqs_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">'(# BLAST processed )(\d+)( .*)'</span><span class="p">,</span> <span class="n" style="color: #333;">pass_info</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">num_sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">num_seqs_match</span><span class="p">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</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="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">buf_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">read_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">raw</span><span class="p">.</span><span class="n" style="color: #333;">read</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_f</span><span class="p">(</span><span class="n" style="color: #333;">buf_size</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">buf</span><span class="p">:</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">buf</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="sa">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_f</span><span class="p">(</span><span class="n" style="color: #333;">buf_size</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">num_sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> </span>
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103
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print log</span></span>
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104
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'PASS'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">num_sequences</span></span>
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105
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'OUTPUT'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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106
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'END'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'AssignGenes'</span></span>
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107
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">printLog</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#9e737285d616e5329acd417dcc52901d591b83d8"><strong>bin/BuildTrees.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">@@ -999,7 +999,7 @@ def runIgPhyML(outfile, igphyml_out, clone_dir, nproc=1, optimization="lr", omeg</td>
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">oformat</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"tab"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">clone_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="python"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Using --clean all with --oformat txt will delete all tree file results.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="python"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"Using --clean all with --oformat txt will <span class="idiff left right">not </span>delete all tree file results.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1003
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="python"> <span class="s" style="color: #d14;">"You'll have to do that yourself."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="python"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">"END"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"IgPhyML analysis"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1323" 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">@@ -1323,19 +1323,17 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC1323" 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;">"""Optimize combination of topology (t) branch lengths (l) and parameters (r), or </span></span>
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="python"><span class="s" style="color: #d14;"> nothing (n), for IgPhyML."""</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="python"> <span class="n" style="color: #333;">igphyml_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;">"--omega"</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;">"omega"</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;">str</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;">"e,e"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1326" 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;">"e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ce"</span><span class="p">,</span> <span class="s" style="color: #d14;">"e,e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ce,e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"e,ce"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ce,ce"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC1326" 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;">"""Omega parameters to estimate for FWR,CDR respectively: </span></span>
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<pre style="margin: 0;">-<span id="LC1328" class="line" lang="python"><span class="s" style="color: #d14;"> e = estimate, ce = estimate + confidence interval"""</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="python"><span class="s" style="color: #d14;"> e = estimate, ce = estimate + confidence interval<span class="idiff left right">, or numeric value</span>"""</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="python"> <span class="n" style="color: #333;">igphyml_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;">"-t"</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;">"kappa"</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;">str</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;">"e"</span><span class="p">,</span></span>
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1330
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<pre style="margin: 0;">-<span id="LC1330" 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;">"e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ce"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC1329" 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;">"""Kappa parameters to estimate: </span></span>
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<pre style="margin: 0;">-<span id="LC1332" class="line" lang="python"><span class="s" style="color: #d14;"> e = estimate, ce = estimate + confidence interval"""</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="python"><span class="s" style="color: #d14;"> e = estimate, ce = estimate + confidence interval<span class="idiff left right">, or numeric value</span>"""</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="python"> <span class="n" style="color: #333;">igphyml_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;">"--motifs"</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;">"motifs"</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;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"WRC_2:0,GYW_0:1,WA_1:2,TW_0:3,SYC_2:4,GRS_0:5"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1333" 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;">"""Which motifs to estimate mutability."""</span><span class="p">)</span></span>
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1334
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="python"> <span class="n" style="color: #333;">igphyml_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;">"--hotness"</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;">"hotness"</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;">str</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;">"e,e,e,e,e,e"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1335" 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;">"""Mutability parameters to estimate: </span></span>
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<pre style="margin: 0;">-<span id="LC1338" class="line" lang="python"><span class="s" style="color: #d14;"> e = estimate, ce = estimate + confidence interval"""</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="python"><span class="s" style="color: #d14;"> e = estimate, ce = estimate + confidence interval<span class="idiff left right">, or numeric value</span>"""</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="python"> <span class="n" style="color: #333;">igphyml_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;">"--oformat"</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;">"oformat"</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;">str</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;">"tab"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1338" 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;">"tab"</span><span class="p">,</span> <span class="s" style="color: #d14;">"txt"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC1339" 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;">"""IgPhyML output format."""</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" 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="118" 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">@@ -118,8 +118,11 @@ def getIDforIMGT(seq_file, imgt_id_len=default_imgt_id_len):</td>
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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="n" style="color: #333;">imgt_id_len</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="n" style="color: #333;">imgt_id_len</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># truncate and replace characters</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">imgt_id_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">49</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># 28 September 2021 (version 1.8.4)</span></span>
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<pre style="margin: 0;">+<span id="LC123" 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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="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;">imgt_id_len</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># older versions</span></span>
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<pre style="margin: 0;">+<span id="LC125" 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;">imgt_id_len</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">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="LC127" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC128" 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="diff-line-num unfold js-unfold new_line" data-linenumber="148" 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">@@ -145,8 +148,8 @@ def writeDb(records, fields, aligner_file, total_count, id_dict=None, annotation</td>
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">AIRRWriter</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="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> Writes parsed records to an output file</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"><span class="s" style="color: #d14;"> records : a iterator of Receptor objects containing alignment data.</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> fields : a list of ordered field names to write.</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> aligner_file : input file name.</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 +358,8 @@ def writeDb(records, fields, aligner_file, total_count, id_dict=None, annotation</td>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC360" 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 class="n" style="color: #333;">imgt_id_len</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="LC361" 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="LC362" class="line" lang="python"> <span class="n" style="color: #333;">imgt_id_len</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="LC363" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC364" 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="LC365" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" 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">@@ -396,7 +400,7 @@ def parseIMGT(aligner_file, seq_file=None, repo=None, cellranger_file=None, part</td>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC401" 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="LC402" 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="n" style="color: #333;">imgt_id_len</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 class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC404" 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="LC405" 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="LC406" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -438,7 +442,7 @@ def parseIMGT(aligner_file, seq_file=None, repo=None, cellranger_file=None, part</td>
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<pre style="margin: 0;"> <span id="LC442" 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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439
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<pre style="margin: 0;"> <span id="LC443" 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="LC444" 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 class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC445" 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="LC446" 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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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</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;">out_args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC448" 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">@@ -535,7 +539,7 @@ def parseIgBLAST(aligner_file, seq_file, repo, amino_acid=False, cellranger_file</td>
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<pre style="margin: 0;"> <span id="LC539" 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="LC540" 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 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 class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC541" 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 class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC542" 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="LC543" 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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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python"> <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;">writer</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</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;">out_args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC545" 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">@@ -614,7 +618,7 @@ def parseIHMM(aligner_file, seq_file, repo, cellranger_file=None, partial=False,</td>
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<pre style="margin: 0;"> <span id="LC618" 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="LC619" 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;">IHMMuneReader</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>
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<pre style="margin: 0;"> <span id="LC620" 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="LC617" 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 class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC621" 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="LC622" 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;">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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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</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;">out_args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC624" 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">@@ -625,7 +629,7 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"><span class="s" style="color: #d14;"> Defines the ArgumentParser.</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"><span class="s" style="color: #d14;"> argparse.ArgumentParser</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dedent</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">@@ -637,34 +641,34 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"><span class="s" style="color: #d14;"> db-fail</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"><span class="s" style="color: #d14;"> database with records that fail due to no productivity information,</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"><span class="s" style="color: #d14;"> no gene V assignment, no J assignment, or no junction region.</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="python"><span class="s" style="color: #d14;"> universal output fields:</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="python"><span class="s" style="color: #d14;"> sequence_id, sequence, sequence_alignment, germline_alignment,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="python"><span class="s" style="color: #d14;"> rev_comp, productive, stop_codon, vj_in_frame, locus,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="python"><span class="s" style="color: #d14;"> v_call, d_call, j_call, junction, junction_length, junction_aa,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="python"><span class="s" style="color: #d14;"> sequence_id, sequence, sequence_alignment, germline_alignment,</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python"><span class="s" style="color: #d14;"> rev_comp, productive, stop_codon, vj_in_frame, locus,</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"><span class="s" style="color: #d14;"> v_call, d_call, j_call, junction, junction_length, junction_aa,</span></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="python"><span class="s" style="color: #d14;"> v_sequence_start, v_sequence_end, v_germline_start, v_germline_end,</span></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"><span class="s" style="color: #d14;"> d_sequence_start, d_sequence_end, d_germline_start, d_germline_end,</span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python"><span class="s" style="color: #d14;"> j_sequence_start, j_sequence_end, j_germline_start, j_germline_end,</span></span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python"><span class="s" style="color: #d14;"> np1_length, np2_length, fwr1, fwr2, fwr3, fwr4, cdr1, cdr2, cdr3</span></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python"><span class="s" style="color: #d14;"> imgt specific output fields:</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python"><span class="s" style="color: #d14;"> n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"><span class="s" style="color: #d14;"> d_frame, v_score, v_identity, d_score, d_identity, j_score, j_identity<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="python"><span class="s" style="color: #d14;"> n1_length, n2_length, p3v_length, p5d_length, p3d_length, p5j_length,</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="python"><span class="s" style="color: #d14;"> d_frame, v_score, v_identity, d_score, d_identity, j_score, j_identity</span></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"><span class="s" style="color: #d14;"> igblast specific output fields:</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"><span class="s" style="color: #d14;"> v_score, v_identity, v_support, v_cigar,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"><span class="s" style="color: #d14;"> d_score, d_identity, d_support, d_cigar,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"><span class="s" style="color: #d14;"> v_score, v_identity, v_support, v_cigar,</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"><span class="s" style="color: #d14;"> d_score, d_identity, d_support, d_cigar,</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"><span class="s" style="color: #d14;"> j_score, j_identity, j_support, j_cigar</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"><span class="s" style="color: #d14;"> ihmm specific output fields:</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"><span class="s" style="color: #d14;"> vdj_score</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python"><span class="s" style="color: #d14;"> 10X specific output fields:</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python"><span class="s" style="color: #d14;"> cell_id, c_call, consensus_count, umi_count,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"><span class="s" style="color: #d14;"> cell_id, c_call, consensus_count, umi_count,</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="python"><span class="s" style="color: #d14;"> v_call_10x, d_call_10x, j_call_10x,</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"><span class="s" style="color: #d14;"> junction_10x, junction_10x_aa</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define ArgumentParser</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__doc__</span><span class="p">,</span> <span class="n" style="color: #333;">epilog</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fields</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CommonHelpFormatter</span><span class="p">,</span> <span class="n" style="color: #333;">add_help</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -686,8 +690,7 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC690" 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;">'Process igblastn output.'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Process igblastn output.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_igblast</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'aligner parsing arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC689" 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;">'-i'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'aligner_files'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC693" 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;">'-i'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'aligner_files'</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="LC694" 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;">'''IgBLAST output files in format 7 with query sequence</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python"><span class="s" style="color: #d14;"> (igblastn argument </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">-outfmt "7 std qseq sseq btop"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">).'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC696" 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;">'-r'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'repo'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -716,18 +719,18 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC719" 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;">'--partial'</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;">'partial'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC720" 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;">'''If specified, include incomplete V(D)J alignments in</span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"><span class="s" style="color: #d14;"> the pass file instead of the fail file. An incomplete alignment</span></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="python"><span class="s" style="color: #d14;"> is defined as a record for which a valid IMGT-gapped sequence<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="python"><span class="s" style="color: #d14;"> cannot be built or that is missing a V gene assignment,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python"><span class="s" style="color: #d14;"> is defined as a record for which a valid IMGT-gapped sequence</span></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python"><span class="s" style="color: #d14;"> cannot be built or that is missing a V gene assignment,</span></span>
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="python"><span class="s" style="color: #d14;"> J gene assignment, junction region, or productivity call.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC725" 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;">'--extended'</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;">'extended'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC723" 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;">'''Specify to include additional aligner specific fields in the output.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC726" 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;">'''Specify to include additional aligner specific fields in the output.</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"><span class="s" style="color: #d14;"> Adds <vdj>_score, <vdj>_identity, <vdj>_support, <vdj>_cigar,</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python"><span class="s" style="color: #d14;"> fwr1, fwr2, fwr3, fwr4, cdr1, cdr2 and cdr3.'''</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;">'--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="LC730" 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="LC731" 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="LC732" 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 class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC733" 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="LC734" 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="LC735" 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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736
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<pre style="margin: 0;"> <span id="LC736" 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">@@ -737,8 +740,7 @@ def getArgParser():</td>
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740
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<pre style="margin: 0;"> <span id="LC740" 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;">'Process igblastp output.'</span><span class="p">,</span></span>
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Process igblastp output.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_igblast_aa</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'aligner parsing arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast_aa</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-i'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'aligner_files'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC743" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast_aa</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-i'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'aligner_files'</span><span class="p">,</span> <span class="n" style="color: #333;">required</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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742
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<pre style="margin: 0;"> <span id="LC744" 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;">'''IgBLAST output files in format 7 with query sequence</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="python"><span class="s" style="color: #d14;"> (igblastp argument </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">-outfmt "7 std qseq sseq btop"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">).'''</span><span class="p">)</span></span>
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast_aa</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-r'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'repo'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -763,7 +765,7 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="python"><span class="s" style="color: #d14;"> the sequence identifiers in the reference sequence set and the IgBLAST</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="python"><span class="s" style="color: #d14;"> database to be exact string matches.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast_aa</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--extended'</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;">'extended'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC766" 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;">'''Specify to include additional aligner specific fields in the output.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC768" 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;">'''Specify to include additional aligner specific fields in the output.</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"><span class="s" style="color: #d14;"> Adds v_score, v_identity, v_support, v_cigar, fwr1, fwr2, fwr3, cdr1 and cdr2.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python"> <span class="n" style="color: #333;">group_igblast_aa</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="LC771" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -779,21 +781,21 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'''Process IMGT/HighV-Quest output</span></span>
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780
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782
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python"><span class="s" style="color: #d14;"> (does not work with V-QUEST).'''</span><span class="p">)</span></span>
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"> <span class="n" style="color: #333;">group_imgt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_imgt</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'aligner parsing arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC782" 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;">'-i'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'aligner_files'</span><span class="p">,</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" 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;">'-i'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'aligner_files'</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff right">,</span></span></span>
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785
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<pre style="margin: 0;"> <span id="LC785" 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;">'''Either zipped IMGT output files (.zip or .txz) or a</span></span>
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"><span class="s" style="color: #d14;"> folder containing unzipped IMGT output files (which must</span></span>
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python"><span class="s" style="color: #d14;"> include 1_Summary, 2_IMGT-gapped, 3_Nt-sequences,</span></span>
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"><span class="s" style="color: #d14;"> and 6_Junction).'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"> <span class="n" style="color: #333;">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;">'-s'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'*'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'seq_files'</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="LC790" 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;">'''List of FASTA files (with .fasta, .fna or .fa</span></span>
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="python"><span class="s" style="color: #d14;"> extension) that were submitted to IMGT/HighV-QUEST.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="python"><span class="s" style="color: #d14;"> extension) that were submitted to IMGT/HighV-QUEST.</span></span>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"><span class="s" style="color: #d14;"> If unspecified, sequence identifiers truncated by IMGT/HighV-QUEST</span></span>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"><span class="s" style="color: #d14;"> will not be corrected.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC794" 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;">'-r'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">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;">'repo'</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="LC795" 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;">'''List of folders and/or fasta files containing</span></span>
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="python"><span class="s" style="color: #d14;"> the germline sequence set used by IMGT/HighV-QUEST.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python"><span class="s" style="color: #d14;"> the germline sequence set used by IMGT/HighV-QUEST.</span></span>
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"><span class="s" style="color: #d14;"> These reference sequences must contain IMGT-numbering spacers (gaps)</span></span>
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="python"><span class="s" style="color: #d14;"> in the V segment. If unspecified, the germline sequence reconstruction<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="python"><span class="s" style="color: #d14;"> in the V segment. If unspecified, the germline sequence reconstruction</span></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="python"><span class="s" style="color: #d14;"> will not be included in the output.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC800" 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;">'--10x'</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;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'cellranger_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC801" 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;">'''Table file containing 10X annotations (with .csv or .tsv</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">@@ -807,17 +809,17 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC809" 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;">'--partial'</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;">'partial'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC810" 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;">'''If specified, include incomplete V(D)J alignments in</span></span>
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python"><span class="s" style="color: #d14;"> the pass file instead of the fail file. An incomplete alignment</span></span>
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="python"><span class="s" style="color: #d14;"> is defined as a record that is missing a V gene assignment,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="python"><span class="s" style="color: #d14;"> is defined as a record that is missing a V gene assignment,</span></span>
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"><span class="s" style="color: #d14;"> J gene assignment, junction region, or productivity call.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC814" 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;">'--extended'</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;">'extended'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC813" 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;">'''Specify to include additional aligner specific fields in the output.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC815" 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;">'''Specify to include additional aligner specific fields in the output.</span></span>
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<pre style="margin: 0;"> <span id="LC816" 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 class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC817" 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="LC818" 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="LC819" 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="LC820" 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 class="idiff left right"> </span></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 class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC821" 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="LC822" 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="LC823" 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="LC824" 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="LC825" 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">@@ -851,18 +853,18 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">group_ihmm</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--partial'</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;">'partial'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC854" 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;">'''If specified, include incomplete V(D)J alignments in</span></span>
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="python"><span class="s" style="color: #d14;"> the pass file instead of the fail file. An incomplete alignment</span></span>
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="python"><span class="s" style="color: #d14;"> is defined as a record for which a valid IMGT-gapped sequence<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="python"><span class="s" style="color: #d14;"> cannot be built or that is missing a V gene assignment,<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="python"><span class="s" style="color: #d14;"> is defined as a record for which a valid IMGT-gapped sequence</span></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"><span class="s" style="color: #d14;"> cannot be built or that is missing a V gene assignment,</span></span>
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="python"><span class="s" style="color: #d14;"> J gene assignment, junction region, or productivity call.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">group_ihmm</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--extended'</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;">'extended'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC858" 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;">'''Specify to include additional aligner specific fields in the output.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC860" 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;">'''Specify to include additional aligner specific fields in the output.</span></span>
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"><span class="s" style="color: #d14;"> Adds the path score of the iHMMune-Align hidden Markov model as vdj_score;</span></span>
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="python"><span class="s" style="color: #d14;"> adds fwr1, fwr2, fwr3, fwr4, cdr1, cdr2 and cdr3.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">parser_ihmm</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;">parseIHMM</span><span class="p">)</span></span>
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"></span>
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span></span>
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"><span class="s" style="color: #d14;"> Parses command line arguments and calls main</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">@@ -881,7 +883,7 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'seq_files'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args_dict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">args_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'seq_files'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'out_files'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args_dict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">args_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'out_files'</span><span class="p">]</span></span>
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'command'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args_dict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">args_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'command'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'func'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args_dict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">args_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'func'</span><span class="p">]</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'func'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args_dict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">args_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'func'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Call main</span></span>
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="s" style="color: #d14;">'aligner_files'</span><span class="p">]):</span></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#b07d9f16b53c7bf45411d329e0d2defdd381c644"><strong>bin/ParseDb.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="142" 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">@@ -142,12 +142,15 @@ def splitDbFile(db_file, field, num_split=None, out_args=default_out_args):</td>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'OUTPUT%i'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">handles_dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'RECORDS'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_count</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'PARTS'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">handles_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'END'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ParseDb'</span></span>
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<pre style="margin: 0;">-<span id="LC146" 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="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Close output file handles</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Close output file handles<span class="idiff left right"> and log file size</span></span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">db_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handles_dict</span><span class="p">:</span> <span class="n" style="color: #333;">handles_dict</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">].</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">handles_dict</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">handles_dict</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">].</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'SIZE%i'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)]</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;">handles_dict</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="p">[</span><span class="s" style="color: #d14;">'END'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ParseDb'</span></span>
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<pre style="margin: 0;">+<span id="LC153" 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="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">handles_dict</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handles_dict</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC156" 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">@@ -364,7 +367,7 @@ def deleteDbFile(db_file, fields, values, logic='any', regex=False,</td>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"><span class="s" style="color: #d14;"> Deletes records from a database file</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"><span class="s" style="color: #d14;"> db_file : the database file name.</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"><span class="s" style="color: #d14;"> fields : a list of fields to check for deletion criteria.</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"><span class="s" style="color: #d14;"> values : a list of values defining deletion targets.</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">@@ -372,8 +375,8 @@ def deleteDbFile(db_file, fields, values, logic='any', regex=False,</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"><span class="s" style="color: #d14;"> regex : if False do exact full string matches; if True allow partial regex matches.</span></span>
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<pre style="margin: 0;"> <span id="LC376" 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="LC377" 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="LC375" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"><span class="s" style="color: #d14;"> str : output file name.</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define string match function</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">@@ -428,14 +431,14 @@ def deleteDbFile(db_file, fields, values, logic='any', regex=False,</td>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">rec_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check for deletion values in all fields</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">delete</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_logic_func</span><span class="p">([</span><span class="n" style="color: #333;">_match_func</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span> <span class="n" style="color: #333;">values</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write sequences</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">delete</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">pass_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">pass_writer</span><span class="p">.</span><span class="n" style="color: #333;">writeDict</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC439" 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="LC440" class="line" lang="python"> <span class="n" style="color: #333;">fail_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print counts</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">printProgress</span><span class="p">(</span><span class="n" style="color: #333;">rec_count</span><span class="p">,</span> <span class="n" style="color: #333;">result_count</span><span class="p">,</span> <span class="mf" style="color: #099;">0.05</span><span class="p">,</span> <span class="n" style="color: #333;">start_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start_time</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</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 +452,7 @@ def deleteDbFile(db_file, fields, values, logic='any', regex=False,</td>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Close file handles</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">pass_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">db_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pass_handle</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC458" 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">@@ -867,10 +870,10 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="python"><span class="s" style="color: #d14;"> Defines the ArgumentParser</span></span>
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:</span></span>
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="python"><span class="s" style="color: #d14;"> None</span></span>
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"><span class="s" style="color: #d14;"> an ArgumentParser object</span></span>
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define input and output field help message</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">@@ -888,7 +891,7 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="python"><span class="s" style="color: #d14;"> required fields:</span></span>
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="python"><span class="s" style="color: #d14;"> sequence_id</span></span>
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define ArgumentParser</span></span>
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__doc__</span><span class="p">,</span> <span class="n" style="color: #333;">epilog</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fields</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CommonHelpFormatter</span><span class="p">,</span> <span class="n" style="color: #333;">add_help</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1027,11 +1030,11 @@ def getArgParser():</td>
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Merges files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="python"> <span class="n" style="color: #333;">group_merge</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_merge</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'parsing arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="python"> <span class="n" style="color: #333;">group_merge</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-o'</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;">'out_file'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1030" 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;">'''Explicit output file name. Note, this argument cannot be used with<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC1033" 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;">'''Explicit output file name. Note, this argument cannot be used with</span></span>
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="python"><span class="s" style="color: #d14;"> the --failed, --outdir or --outname arguments.'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="python"> <span class="n" style="color: #333;">group_merge</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--drop'</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;">'drop'</span><span class="p">,</span></span>
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1033
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1036
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<pre style="margin: 0;"> <span id="LC1036" 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;">'''If specified, drop fields that do not exist in all input files.</span></span>
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1034
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<pre style="margin: 0;">-<span id="LC1034" class="line" lang="python"><span class="s" style="color: #d14;"> Otherwise, include all columns in all files and fill missing data<span class="idiff left right"> </span></span></span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="python"><span class="s" style="color: #d14;"> Otherwise, include all columns in all files and fill missing data</span></span>
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1035
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="python"><span class="s" style="color: #d14;"> with empty strings.'''</span><span class="p">)</span></span>
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1036
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="python"> <span class="n" style="color: #333;">parser_merge</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;">mergeDbFiles</span><span class="p">)</span></span>
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1037
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1092" 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="1095" 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">@@ -1092,4 +1095,4 @@ if __name__ == '__main__':</td>
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1092
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1095
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<pre style="margin: 0;"> <span id="LC1095" class="line" lang="python"> <span class="n" style="color: #333;">args_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'out_file'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="s" style="color: #d14;">'out_files'</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> \</span>
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<td class="old_line diff-line-num" data-linenumber="1093" 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">
1093
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<td class="new_line diff-line-num" data-linenumber="1096" 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">
1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="s" style="color: #d14;">'out_files'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="old_line diff-line-num" data-linenumber="1094" 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">
1094
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1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">func</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">args_dict</span><span class="p">)</span></span>
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1095
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<pre style="margin: 0;">-<span id="LC1095" class="line" lang="python"><span class="idiff left right"> </span></span></pre>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#644e37c5303095d9570d84c455cb6822d50aa50e"><strong>changeo.egg-info/PKG-INFO</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: changeo</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.<span class="idiff left right">1</span>.0</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 1.<span class="idiff left right">2</span>.0</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://changeo.readthedocs.io</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Namita Gupta, Jason Anthony Vander Heiden</span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#1f4dd37096d2ddfcb225023d881d7065285142c4"><strong>changeo.egg-info/requires.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,5 +4,5 @@ pandas>=0.24</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">biopython>=1.77</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">PyYAML>=5.1</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">setuptools>=2.0</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">presto>=0.<span class="idiff left right">6.2</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">presto>=0.<span class="idiff left right">7.0</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">airr>=1.3.1</span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#05fdcdf376e61bb9ea4aa991f73cfd29b5aa07b3"><strong>changeo/IO.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,11 +13,12 @@ import yaml</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">zipfile</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="n" style="color: #333;">groupby</span><span class="p">,</span> <span class="n" style="color: #333;">zip_longest</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TemporaryDirectory</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">textwrap</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">indent</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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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="LC20" 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;">getFileType</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>
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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.IO</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">getFileType</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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">printDebug</span></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;">changeo.Defaults</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">default_csv_size</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.Gene</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">getAllele</span><span class="p">,</span> <span class="n" style="color: #333;">getLocus</span><span class="p">,</span> <span class="n" style="color: #333;">getVAllele</span><span class="p">,</span> <span class="n" style="color: #333;">getDAllele</span><span class="p">,</span> <span class="n" style="color: #333;">getJAllele</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.Receptor</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AIRRSchema</span><span class="p">,</span> <span class="n" style="color: #333;">AIRRSchemaAA</span><span class="p">,</span> <span class="n" style="color: #333;">ChangeoSchema</span><span class="p">,</span> <span class="n" style="color: #333;">ChangeoSchemaAA</span><span class="p">,</span> <span class="n" style="color: #333;">Receptor</span><span class="p">,</span> <span class="n" style="color: #333;">ReceptorData</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">@@ -2167,13 +2168,14 @@ class IHMMuneReader:</td>
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2168
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<pre style="margin: 0;"> <span id="LC2168" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">db</span></span>
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<pre style="margin: 0;"> <span id="LC2169" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC2170" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC2170" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readGermlines</span><span class="p">(</span><span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">asis</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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2171
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<pre style="margin: 0;">+<span id="LC2171" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readGermlines</span><span class="p">(</span><span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">asis</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">warn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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2171
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2172
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<pre style="margin: 0;"> <span id="LC2172" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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2172
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2173
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<pre style="margin: 0;"> <span id="LC2173" class="line" lang="python"><span class="s" style="color: #d14;"> Parses germline repositories</span></span>
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2173
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2174
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<pre style="margin: 0;"> <span id="LC2174" class="line" lang="python"></span>
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2174
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2175
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<pre style="margin: 0;"> <span id="LC2175" class="line" lang="python"><span class="s" style="color: #d14;"> Arguments:</span></span>
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2175
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2176
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<pre style="margin: 0;"> <span id="LC2176" class="line" lang="python"><span class="s" style="color: #d14;"> references (list): list of strings specifying directories and/or files from which to read germline records.</span></span>
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2177
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<pre style="margin: 0;"> <span id="LC2177" class="line" lang="python"><span class="s" style="color: #d14;"> asis (bool): if True use sequence ID as record name and do not parse headers for allele names.</span></span>
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<pre style="margin: 0;">+<span id="LC2178" class="line" lang="python"><span class="s" style="color: #d14;"> warn (bool): print warning messages to standard error if True.</span></span>
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2177
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2179
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<pre style="margin: 0;"> <span id="LC2179" class="line" lang="python"></span>
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2180
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<pre style="margin: 0;"> <span id="LC2180" class="line" lang="python"><span class="s" style="color: #d14;"> Returns:</span></span>
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2181
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<pre style="margin: 0;"> <span id="LC2181" class="line" lang="python"><span class="s" style="color: #d14;"> dict: Dictionary of germlines in the form {allele: sequence}.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2194" 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">@@ -2194,12 +2196,20 @@ def readGermlines(references, asis=False):</td>
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2196
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<pre style="margin: 0;"> <span id="LC2196" class="line" lang="python"> <span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="s" style="color: #d14;">'No valid germline fasta files (.fasta, .fna, .fa) were found at %s.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">references</span><span class="p">))</span></span>
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2197
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<pre style="margin: 0;"> <span id="LC2197" class="line" lang="python"></span>
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2198
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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="python"> <span class="n" style="color: #333;">repo_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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2199
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<pre style="margin: 0;">+<span id="LC2199" class="line" lang="python"> <span class="n" style="color: #333;">duplicates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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2197
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2200
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<pre style="margin: 0;"> <span id="LC2200" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">file_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">repo_files</span><span class="p">:</span></span>
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2198
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2201
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<pre style="margin: 0;"> <span id="LC2201" 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;">file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">'rU'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">file_handle</span><span class="p">:</span></span>
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2199
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2202
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<pre style="margin: 0;"> <span id="LC2202" class="line" lang="python"> <span class="n" style="color: #333;">germlines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">file_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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2203
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<pre style="margin: 0;"> <span id="LC2203" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">germlines</span><span class="p">:</span></span>
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2201
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2204
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<pre style="margin: 0;"> <span id="LC2204" class="line" lang="python"> <span class="n" style="color: #333;">germ_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getAllele</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">,</span> <span class="s" style="color: #d14;">'first'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">asis</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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2202
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<pre style="margin: 0;">-<span id="LC2202" class="line" lang="python"> <span class="n" style="color: #333;">repo_dict</span><span class="p">[</span><span class="n" style="color: #333;">germ_key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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2205
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<pre style="margin: 0;">+<span id="LC2205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">germ_key</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;">repo_dict</span><span class="p">:</span></span>
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2206
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<pre style="margin: 0;">+<span id="LC2206" class="line" lang="python"> <span class="n" style="color: #333;">repo_dict</span><span class="p">[</span><span class="n" style="color: #333;">germ_key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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2207
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<pre style="margin: 0;">+<span id="LC2207" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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2208
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<pre style="margin: 0;">+<span id="LC2208" class="line" lang="python"> <span class="n" style="color: #333;">duplicates</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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2209
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<pre style="margin: 0;">+<span id="LC2209" class="line" lang="python"></span>
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2210
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<pre style="margin: 0;">+<span id="LC2210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">warn</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">duplicates</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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2211
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<pre style="margin: 0;">+<span id="LC2211" class="line" lang="python"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indent</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">duplicates</span><span class="p">),</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">9</span><span class="p">)</span></span>
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2212
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<pre style="margin: 0;">+<span id="LC2212" class="line" lang="python"> <span class="n" style="color: #333;">printWarning</span><span class="p">(</span><span class="s" style="color: #d14;">'Duplicated germline allele names excluded from references:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">w</span><span class="p">)</span></span>
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2203
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2213
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<pre style="margin: 0;"> <span id="LC2213" class="line" lang="python"></span>
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2204
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2214
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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">repo_dict</span></span>
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2215
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<pre style="margin: 0;"> <span id="LC2215" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#39d40dda335856b0a31785a995858f9160602e82"><strong>changeo/Version.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,5 +5,5 @@ Version and authorship information</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__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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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__copyright__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Copyright 2021 Kleinstein Lab, Yale University. All rights reserved.'</span></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="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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8
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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</span>.0'</span></span>
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9
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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">6</span>.2<span class="idiff right">1</span>'</span></span></pre>
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8
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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">2</span>.0'</span></span>
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9
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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.<span class="idiff left">1</span>0.2<span class="idiff right">9</span>'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/changeo/-/commit/da695a88ac5d3597e58301e55cda02ee5771f446#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,5 +4,5 @@ pandas>=0.24</td>
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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>>=1.77</span>
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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>>=5.1</span>
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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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/presto" rel="nofollow noreferrer noopener" target="_blank">presto</a>>=0.<span class="idiff left right">6.2</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/presto" rel="nofollow noreferrer noopener" target="_blank">presto</a>>=0.<span class="idiff left right">7.0</span></span>
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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>>=1.3.1</span></pre>
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