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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-cgecore">Debian Med / python-cgecore</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cgecore/-/commit/3b828448931a7035f0affbb71dba36a919d63356">3b828448</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-03-17T13:15:13+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cgecore/-/commit/918eda8f21120c7b534a3d24024eee7c2cb23bf2">918eda8f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-03-17T13:23:57+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.3+ds</pre>
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#7b0252816f84a9bb50c75dd39e7965dae35692ce">
<span class="deleted-file">
−
cgecore.egg-info/PKG-INFO
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<li class="file-stats">
<a href="#1e0dc2619616ff2077b3b6e2ce41a896bb080366">
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cgecore.egg-info/SOURCES.txt
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<a href="#4074ea75bfce6f2c042a33c88eb68b4afbde65e0">
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−
cgecore.egg-info/dependency_links.txt
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<a href="#aecbca4ffe76ae2941149e093422060ca914072e">
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cgecore.egg-info/top_level.txt
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<a href="#99e6b3e9b6332ede61f0c761ad90306a89039e05">
cgecore/__init__.py
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<li class="file-stats">
<a href="#81293046cfcd19d3582f14835e080d2d680f9865">
cgecore/blaster/blaster.py
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<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.0</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: cgecore</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.5.<span class="idiff left right">2</span></span>
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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="LC3" class="line" lang="plaintext">Version: 1.5.<span class="idiff left right">3</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Center for Genomic Epidemiology Core Module</span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext">Author: Center for Genomic Epidemiology</span>
</pre>
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</li>
<li id="7b0252816f84a9bb50c75dd39e7965dae35692ce">
<a href="https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2#7b0252816f84a9bb50c75dd39e7965dae35692ce"><strong>cgecore.egg-info/PKG-INFO</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.0</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Name: cgecore</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.5.2</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Summary: Center for Genomic Epidemiology Core Module</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Author: Center for Genomic Epidemiology</span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">Author-email: cgehelp@cbs.dtu.dk</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: Apache License, Version 2.0</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Description: # cge_core_module</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"> Core module for the Center for Genomic Epidemiology</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> </span>
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<td class="diff-line-num old old_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> This module contains classes and functions needed to run the service wrappers and pipeline scripts</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> The pypi project can be found here:</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> https://pypi.org/project/cgecore/</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> # How to update:</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> 1. Make changes to the modules</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> 2. Bump the version number accordingly in cgecore/__init__.py</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> 3. Install package locally</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> 4. Test the changes locally (for both python2 and python3)</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> 5. Distribute to Pypi</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> # Install package locally</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> python2 setup.py install</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> python3 setup.py install</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> # Distribute to PyPi</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> python3 setup.py sdist bdist_wheel</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> twine upload dist/*</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> *deprecated:*</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> ~~python setup.py sdist upload -r pypi~~</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">Platform: UNKNOWN</span></pre>
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<li id="1e0dc2619616ff2077b3b6e2ce41a896bb080366">
<a href="https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2#1e0dc2619616ff2077b3b6e2ce41a896bb080366"><strong>cgecore.egg-info/SOURCES.txt</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">setup.py</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">cgecore.egg-info/PKG-INFO</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">cgecore.egg-info/SOURCES.txt</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">cgecore.egg-info/dependency_links.txt</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">cgecore/blaster/__init__.py</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">cgecore/organisminfo/__init__.py</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">cgecore/organisminfo/gram_neg.txt</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">cgecore/organisminfo/gram_pos.txt</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">cgecore/organisminfo/gramstain.py</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">cgecore/organisminfo/species.py</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2#4074ea75bfce6f2c042a33c88eb68b4afbde65e0"><strong>cgecore.egg-info/dependency_links.txt</strong>
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<a href="https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2#99e6b3e9b6332ede61f0c761ad90306a89039e05"><strong>cgecore/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ from .argumentparsing import (check_file_type, get_arguments, get_string,</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#####################</span></span>
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<pre style="margin: 0;">-<span id="LC16" 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;">"1.5.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.5.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"argumentparsing"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"cmdline"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2#81293046cfcd19d3582f14835e080d2d680f9865"><strong>cgecore/blaster/blaster.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">@@ -194,31 +194,32 @@ class Blaster():</td>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">'strand'</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="s" style="color: #d14;">'perc_coverage'</span><span class="p">:</span> <span class="n" style="color: #333;">perc_coverage</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Saving the result if any</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">best_hsp</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">save</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="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If there are other gene alignments they are compared</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_results</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">tmp_gene_split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_split</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">tmp_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_results</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Compare the hit results</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">save</span><span class="p">,</span> <span class="n" style="color: #333;">gene_split</span><span class="p">,</span> <span class="n" style="color: #333;">gene_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">compare_results</span><span class="p">(</span><span class="n" style="color: #333;">save</span><span class="p">,</span> <span class="n" style="color: #333;">best_hsp</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">tmp_results</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">allowed_overlap</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the hit is not overlapping with other hit</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seqeunces it is kept</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">save</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># DEBUG</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Saving: {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">hit_id</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">gene_results</span><span class="p">[</span><span class="n" style="color: #333;">hit_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">best_hsp</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">best_hsp</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Saving the result if any</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">best_hsp</span><span class="p">:</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">save</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="LC204" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If there are other gene alignments they are compared</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_results</span><span class="p">:</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">tmp_gene_split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_split</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">tmp_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_results</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Compare the hit results</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">save</span><span class="p">,</span> <span class="n" style="color: #333;">gene_split</span><span class="p">,</span> <span class="n" style="color: #333;">gene_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">compare_results</span><span class="p">(</span><span class="n" style="color: #333;">save</span><span class="p">,</span> <span class="n" style="color: #333;">best_hsp</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">tmp_results</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">allowed_overlap</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the hit is not overlapping with other hit</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seqeunces it is kept</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">save</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># DEBUG</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Saving: {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">hit_id</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">gene_results</span><span class="p">[</span><span class="n" style="color: #333;">hit_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">best_hsp</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">result_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC225" 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">@@ -463,7 +464,7 @@ class Blaster():</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If new_score == old_score but identity and coverages are not the same.</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># which gene should be chosen?? Now they are both ke<span class="idiff left right">e</span>pt.</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># which gene should be chosen?? Now they are both kept.</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Save a split if the new hit creats one - both</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># hits are saved</span></span>
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