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GitLab

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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/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8">422e7b5e</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2020-01-06T17:33:00+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.2</pre>

</li>

</ul>

<h4>5 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

PKG-INFO

</a>

</li>

<li class="file-stats">

<a href="#7b0252816f84a9bb50c75dd39e7965dae35692ce">

cgecore.egg-info/PKG-INFO

</a>

</li>

<li class="file-stats">

<a href="#99e6b3e9b6332ede61f0c761ad90306a89039e05">

cgecore/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#81293046cfcd19d3582f14835e080d2d680f9865">

cgecore/blaster/blaster.py

</a>

</li>

<li class="file-stats">

<a href="#f48e9597dc324478eec05b1d6d11a14a9c1d98b2">

cgecore/cgefinder.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

<a href="https://salsa.debian.org/med-team/python-cgecore/commit/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.0</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: cgecore</span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.5.<span class="idiff left right">0</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

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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">2</span></span>

</pre>

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4

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Center for Genomic Epidemiology Core Module</span>

</pre>

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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">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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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>

</pre>

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6

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<td class="diff-line-num new_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">

6

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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>

</td>

</tr>

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<br>

</li>

<li id="7b0252816f84a9bb50c75dd39e7965dae35692ce">

<a href="https://salsa.debian.org/med-team/python-cgecore/commit/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8#7b0252816f84a9bb50c75dd39e7965dae35692ce"><strong>cgecore.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: 1.0</span>

</pre>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: cgecore</span>

</pre>

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3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 1.5.<span class="idiff left right">0</span></span>

</pre>

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3

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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">2</span></span>

</pre>

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4

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Center for Genomic Epidemiology Core Module</span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<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">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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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>

</pre>

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6

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<td class="diff-line-num new_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">

6

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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>

</td>

</tr>

</table>

<br>

</li>

<li id="99e6b3e9b6332ede61f0c761ad90306a89039e05">

<a href="https://salsa.debian.org/med-team/python-cgecore/commit/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8#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>

</pre>

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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">0</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">2</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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<br>

</li>

<li id="81293046cfcd19d3582f14835e080d2d680f9865">

<a href="https://salsa.debian.org/med-team/python-cgecore/commit/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8#81293046cfcd19d3582f14835e080d2d680f9865"><strong>cgecore/blaster/blaster.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" 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="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,7 +98,6 @@ class Blaster():</td>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="99" 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="LC99" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Parsing over the hits and only keeping the best</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">blast_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">blast_records</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># OLD CODE TO BE REMOVED</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#  query = blast_record.query</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#  blast_record.alignments.sort(key=lambda align: (</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" 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="112" 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">@@ -113,7 +112,6 @@ class Blaster():</td>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">                    <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">align</span><span class="p">:</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">((</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">hsp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">identities</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python">                                           <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hsp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hsps</span><span class="p">))),</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python">                    <span class="n" style="color: #333;">reverse</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="LC116" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">                <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blast_record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">alignment</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">blast_record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">alignments</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">@@ -121,13 +119,13 @@ class Blaster():</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># HSP fragment</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">                    <span class="n" style="color: #333;">best_e_value</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="LC121" class="line" lang="python">                    <span class="n" style="color: #333;">best_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">                    <span class="n" style="color: #333;">start_hsp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python">                    <span class="n" style="color: #333;">end_hsp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hsp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">hsps</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hsp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expect</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">best_e_value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">hsp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bits</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">best_bit</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python">                            <span class="n" style="color: #333;">best_e_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hsp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expect</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python">                            <span class="n" style="color: #333;">best_bit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hsp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bits</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># best_e_value = hsp.expect</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># best_bit = hsp.bits</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">                            <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">                            <span class="n" style="color: #333;">sbjct_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># DEBUG</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="158" 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="156" 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">@@ -158,7 +156,6 @@ class Blaster():</td>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">                            <span class="n" style="color: #333;">hit_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s..</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">                                <span class="n" style="color: #333;">contig_name</span><span class="p">,</span> <span class="n" style="color: #333;">query_start</span><span class="p">,</span> <span class="n" style="color: #333;">query_end</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="160" 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="LC158" class="line" lang="python">                                <span class="n" style="color: #333;">sbjct_header</span><span class="p">,</span> <span class="n" style="color: #333;">cal_score</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="159" 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="LC161" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="162" 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="LC159" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># If the hit is on the other strand</span></span>

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<td class="diff-line-num old_line" data-linenumber="163" 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="LC160" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sbjct_start</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sbjct_end</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="164" 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="LC161" class="line" lang="python">                                <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sbjct_start</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" 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="195" 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">@@ -198,29 +195,30 @@ class Blaster():</td>

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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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<td class="diff-line-num old old_line" data-linenumber="201" 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="diff-line-num new_line old" data-linenumber="198" 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="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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<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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<td class="diff-line-num old old_line" data-linenumber="205" 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="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>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="198" 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="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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<td class="diff-line-num old old_line" data-linenumber="207" 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="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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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" 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="LC210" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># Compare the hit results</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="211" 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="LC211" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="212" 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="LC212" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="213" 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="LC213" class="line" lang="python">                                                     <span class="n" style="color: #333;">tmp_results</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python">                                                     <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">                                                     <span class="n" style="color: #333;">allowed_overlap</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python">                            <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="218" 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="LC218" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># If the hit is not overlapping with other hit</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="219" 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="diff-line-num new_line old" data-linenumber="198" 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="LC219" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># seqeunces it is kept</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="220" 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="LC220" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="221" 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="LC221" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># DEBUG</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" 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="diff-line-num new_line old" data-linenumber="198" 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="LC222" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="223" 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="diff-line-num new_line old" data-linenumber="198" 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="LC223" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="198" 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="LC198" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="199" 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="LC199" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" 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="LC200" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Saving the result if any</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="201" 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="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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="207" 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="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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="208" 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="LC208" class="line" lang="python">                                <span class="c1" style="color: #998; font-style: italic;"># Compare the hit results</span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="210" 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="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>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python">                                <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"></span>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="218" 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="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>

</pre>

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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>

</pre>

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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>

</pre>

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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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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC223" 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="LC224" 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">@@ -326,15 +324,23 @@ class Blaster():</td>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">            <span class="n" style="color: #333;">old_HSP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit_data</span><span class="p">[</span><span class="s" style="color: #d14;">'HSP_length'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python">            <span class="n" style="color: #333;">remove_old</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># If they align to the same gene in the database they are</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># compared</span></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">new_db_hit</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">old_db_hit</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># If the hit provids additional sequence it is kept and</span></span>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#If the hit comes from different contig</span></span>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">old_contig</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">new_contig</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Save a split if the new hit still creats one</span></span>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">new_db_hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp_gene_split</span></span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python">                       <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">hit_id</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;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">new_db_hit</span><span class="p">]):</span></span>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python">                        <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">new_db_hit</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="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># If the hit provides additional sequence it is kept and</span></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># the new coverage is saved otherwise the one with the</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># highest score is kept</span></span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">new_start_sbjct</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">old_start_sbjct</span></span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python">                <span class="k" style="font-weight: 600;"><span class="idiff left right">el</span>if</span><span class="p">(</span><span class="n" style="color: #333;">new_start_sbjct</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">old_start_sbjct</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python">                   <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">new_end_sbjct</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">old_end_sbjct</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># Save the hits as split</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">@@ -342,28 +348,29 @@ class Blaster():</td>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hit</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;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">old_db_hit</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python">                        <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">old_db_hit</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">]</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="LC350" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC345" 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="LC346" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">new_score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">old_score</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                else:</span></span>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                    if new_score > old_score:</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Set to remove old hit</span></span>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python">                        <span class="n" style="color: #333;">remove_old</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="LC355" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                        remove_old = 1</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Save a split if the new hit still creats one</span></span>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">new_db_hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp_gene_split</span></span>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python">                           <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">hit_id</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;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">new_db_hit</span><span class="p">]):</span></span>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                        if(new_db_hit in tmp_gene_split</span></span>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                           and hit_id not in tmp_gene_split[new_db_hit]):</span></span>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python">                            <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">new_db_hit</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="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">-<span id="LC355" 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="LC356" 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;">0</span></span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                            tmp_gene_split[new_db_hit][hit_id] = 1</span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                    else:</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                        save = 0</span></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># If the old and new hit is not identical the</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># possible saved gene split for the new hit is</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># removed</span></span>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hit_id</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">hit</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">new_db_hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp_gene_split</span></span>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python">                               <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">hit_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">new_db_hit</span><span class="p">]):</span></span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                        if hit_id != hit:</span></span>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                            if(new_db_hit in tmp_gene_split</span></span>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                               and hit_id in tmp_gene_split[new_db_hit]):</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python">                                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">tmp_gene_split</span><span class="p">[</span><span class="n" style="color: #333;">new_db_hit</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="LC366" class="line" lang="python">                        <span class="k" style="font-weight: 600;">break</span></span>

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                                del tmp_gene_split[new_db_hit][hit_id]</span></span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>                        break</span></span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># If the hits comes form the same part of the contig</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># sequnce but match different genes only the best hit is</span></span>

</pre>

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<br>

</li>

<li id="f48e9597dc324478eec05b1d6d11a14a9c1d98b2">

<a href="https://salsa.debian.org/med-team/python-cgecore/commit/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8#f48e9597dc324478eec05b1d6d11a14a9c1d98b2"><strong>cgecore/cgefinder.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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="36" 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">@@ -36,9 +36,28 @@ class CGEFinder():</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">            <span class="n" style="color: #333;">kma_apm</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;">kma_memmode</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;">kma_nanopore</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;">debug</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="LC37" class="line" lang="python">            <span class="n" style="color: #333;">kma_add_args</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;">kma_cge</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;">kma_1t1</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;">           I expect that there will only be one hit pr gene, but if there are</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;">           TODO: Result storage - Too complex. Not effective.</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;">           Before changing code: Check downstream dependencies of results</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;">                                 dicts.</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;">           Currently the code stores results in four different dicts. This can</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;">           be reduced to just one.</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;">           The main dict that stores all results currently stores one result pr</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;">           hit, and distiguishes hits to the same gene by adding an increasing</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;">           integer (obtained by getting the length of the internal gene dict).</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;">           The main dict also stores an internal dict for each 'gene'</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;">           containing an empty dict for each hit.</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;">           Solution: Create a main<dict> -> gene<list> -> hit<dict> design, and</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;">           remove all the references main -> hit. This reduces redundancy and</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;">           the need for manipulating gene names with an incremental integer.</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;">           TODO: Method too many responsibilities</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;">           Solution: Create KMA class, create additional functions.</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;">           Original comment:</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;">           "I expect that there will only be one hit pr gene, but if there are</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;">           more, I assume that the sequence of the hits are the same in the res</span></span>

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<td class="diff-line-num new_line old" data-linenumber="59" 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="LC41" class="line" lang="python"><span class="s" style="color: #d14;">           file and the aln file.</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;">           file and the aln file."</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;">           Not sure if this holds for the current code.</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">        <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python">        <span class="n" style="color: #333;">min_cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_cov</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" 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="136" 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">@@ -117,16 +136,24 @@ class CGEFinder():</td>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">                         <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</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="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python">                                           <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">)))</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python">            <span class="n" style="color: #333;">gene_res_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res_file</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'No hit found'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python">                    <span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># kma_results[db]["excluded"] = dict()</span></span>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># continue</span></span>

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<td class="diff-line-num new_line" data-linenumber="145" 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="LC145" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="146" 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="LC146" class="line" lang="python">                <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">data</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">                <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="149" 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="LC149" class="line" lang="python">                <span class="n" style="color: #333;">gene_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_res_count</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python">                <span class="n" style="color: #333;">gene_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_count</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" 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="LC151" class="line" lang="python">                <span class="n" style="color: #333;">gene_res_count</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_count</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" 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="LC152" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gene_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="python">                    <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="155" 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="LC155" class="line" lang="python">                    <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}_{}"</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;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">gene_count</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="157" 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="LC157" class="line" lang="python">                <span class="n" style="color: #333;">sbjct_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python">                <span class="n" style="color: #333;">sbjct_ident</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">                <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="134" 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="161" 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">@@ -134,11 +161,6 @@ class CGEFinder():</td>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">                <span class="n" style="color: #333;">q_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">data</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>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">                <span class="n" style="color: #333;">p_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">[</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="LC163" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" 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="LC137" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene</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;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="164" 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="LC138" class="line" lang="python">                    <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="139" 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="LC139" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="140" 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="diff-line-num new_line old" data-linenumber="164" 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="LC140" class="line" lang="python">                    <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">gene</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"></span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">                <span class="n" style="color: #333;">exclude_reasons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="144" 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="LC166" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_cov</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sbjct_ident</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">threshold</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,7 +168,6 @@ class CGEFinder():</td>

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<td class="diff-line-num old_line" data-linenumber="146" 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="LC168" class="line" lang="python">                    <span class="n" style="color: #333;">exclude_reasons</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">sbjct_ident</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="170" 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="LC170" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">exclude_reasons</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" 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="diff-line-num new_line old" data-linenumber="171" 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="LC149" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># kma_results[db]["excluded"][hit] = exclude_reasons</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="171" 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="LC171" class="line" lang="python">                    <span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="s" style="color: #d14;">"excluded"</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exclude_reasons</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="172" 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="LC172" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="173" 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="LC173" class="line" lang="python">                <span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" 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="192" 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">@@ -171,7 +192,7 @@ class CGEFinder():</td>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="172" 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="LC193" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Open align file</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" 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="LC194" 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;">align_filename</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;">align_file</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" 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="diff-line-num new_line old" data-linenumber="195" 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="LC174" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left">hit_no</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">dict</span></span><span class="p"><span class="idiff right">()</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="195" 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="LC195" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left">gene_aln_count</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{}</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" 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">

175

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<td class="diff-line-num new_line" data-linenumber="196" 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="LC196" class="line" lang="python">                <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" 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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197

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Parse through alignments</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="198" 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="LC198" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">align_file</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" 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="204" 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">@@ -183,17 +204,13 @@ class CGEFinder():</td>

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<td class="diff-line-num new_line" data-linenumber="204" 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="LC204" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="205" 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">

205

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python">                        <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</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="n" style="color: #333;">strip</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="206" 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="LC206" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="186" 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="diff-line-num new_line old" data-linenumber="207" 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="LC186" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene</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;">hit_no</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="207" 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="LC187" class="line" lang="python">                            <span class="n" style="color: #333;">hit_no</span><span class="p">[</span><span class="n" style="color: #333;">gene</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="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" 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="diff-line-num new_line old" data-linenumber="207" 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="LC188" class="line" lang="python">                        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="189" 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="diff-line-num new_line old" data-linenumber="207" 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="LC189" class="line" lang="python">                            <span class="n" style="color: #333;">hit_no</span><span class="p">[</span><span class="n" style="color: #333;">gene</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">hit_no</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="190" 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="diff-line-num new_line old" data-linenumber="207" 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="LC190" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="207" 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="LC207" class="line" lang="python">                        <span class="n" style="color: #333;">gene_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_aln_count</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python">                        <span class="n" style="color: #333;">gene_aln_count</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_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="LC209" 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="LC192" class="line" lang="python">                        <span class="c1" style="color: #998; font-style: italic;"># Check if gene one of the user specified genes</span></span>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hit_no</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'1'</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gene_aln_count</span><span class="p">[</span><span class="n" style="color: #333;">gene</span><span class="p">]</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="LC211" class="line" lang="python">                            <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span></span>

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<pre style="margin: 0;"> <span id="LC212" 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="LC196" class="line" lang="python">                            <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">gene</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hit_no</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">gene</span></span><span class="p"><span class="idiff right">]</span></span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python">                            <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">"{}_{}"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gene</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gene_aln_count</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">gene</span></span><span class="p"><span class="idiff right">])</span></span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python">                            <span class="n" style="color: #333;">line_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)[</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;">strip</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" 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="226" 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">@@ -209,7 +226,7 @@ class CGEFinder():</td>

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<pre style="margin: 0;"> <span id="LC226" 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="LC227" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" not in results: "</span><span class="p">,</span> <span class="n" style="color: #333;">kma_results</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># concatinate all sequence<span class="idiff left right">s</span> lists and find subject start</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># concatinate all sequence lists and find subject start</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># and subject end</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">            <span class="n" style="color: #333;">gene_align_sbjct</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" 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="234" 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">@@ -217,8 +234,6 @@ class CGEFinder():</td>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python">            <span class="n" style="color: #333;">gene_align_homo</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</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;"># if(hit == "excluded"):</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># continue</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python">                <span class="n" style="color: #333;">align_sbjct</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">'sbjct_string'</span><span class="p">])</span></span>

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<td class="diff-line-num new_line" data-linenumber="238" 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="LC238" class="line" lang="python">                <span class="n" style="color: #333;">align_query</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">'query_string'</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">                <span class="n" style="color: #333;">align_homo</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">kma_results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">'homo_string'</span><span class="p">])</span></span>

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