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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/gubbins">Debian Med / gubbins</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3">099d3934</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-11T10:59:32+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.1.0</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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</li>
<li class="file-stats">
<a href="#0e20753a4c88045119953fc070aa994389074a00">
python/gubbins/ValidateFastaAlignment.py
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<li class="file-stats">
<a href="#aaaba74cad9a3f815206ba8bf91e26f24eb5a22a">
python/gubbins/common.py
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<li class="file-stats">
<a href="#7fda0caa14793966c396bc00135eaa6633fb5b4f">
python/gubbins/pyjar.py
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<li class="file-stats">
<a href="#d647c87bee00bdb39a6f51342867cc4d0f2c460d">
python/gubbins/run_gubbins.py
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<li class="file-stats">
<a href="#b37728bccd07a22008bf25dd8e4521fc8d157087">
python/gubbins/treebuilders.py
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<li class="file-stats">
<a href="#0452b1f8c4d2a44bb544f6ac29fc88719de5614e">
python/gubbins/utils.py
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<li class="file-stats">
<a href="#364cbe5725a887b7cfe83f41addc60bf817a431d">
<span class="new-file">
+
python/scripts/extract_clade.py
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<li class="file-stats">
<a href="#736ae1bee457a1fb132cee635e1205a31bf0f0a5">
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+
python/scripts/generate_ska_alignment.py
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<li class="file-stats">
<a href="#73997306d4f22caca12478c8d6748a2653289fe5">
<span class="new-file">
+
python/scripts/mask_gubbins_aln.py
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<h4>Changes:</h4>
<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">
<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">3.<span class="idiff left right">0</span>.0</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.<span class="idiff left right">1</span>.0</span></pre>
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<br>
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<li id="0e20753a4c88045119953fc070aa994389074a00">
<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#0e20753a4c88045119953fc070aa994389074a00"><strong>python/gubbins/ValidateFastaAlignment.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@ from collections import Counter</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="8" 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="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ValidateFastaAlignment</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">input_filename</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">input_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_filename</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +23,8 @@ class ValidateFastaAlignment(object):</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">does_each_sequence_have_a_name_and_genomic_data</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC29" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">input_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;">input_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">input_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</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">@@ -33,21 +33,19 @@ class ValidateFastaAlignment(object):</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">number_of_sequences</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="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Error with the input FASTA file: <span class="idiff right">One of the sequence names</span> is blank"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">write</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Error with the input FASTA file: <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">record</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</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> is blank</span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Error with the input FASTA file: <span class="idiff right">One of the sequences</span> is empty"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">write</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Error with the input FASTA file: <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">record</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</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> is empty</span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">'[^ACGTNacgtn-]'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Error with the input FASTA file: <span class="idiff">One of the sequences</span> contains <span class="idiff right">o</span>dd characters, only ACGTNacgtn- are permitted"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">write</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Error with the input FASTA file: <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">record</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</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> contains d<span class="idiff">isallowe</span>d characters, only ACGTNacgtn- are permitted</span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">input_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">does_each_sequence_have_the_same_length</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC48" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">input_filename</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">input_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">input_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">sequence_length</span> <span class="o" style="font-weight: 600;">=</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="LC51" 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;">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">@@ -63,17 +61,25 @@ class ValidateFastaAlignment(object):</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error with the input FASTA file: It is in the wrong format so check its an alignment"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">are_sequence_names_unique</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">with</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">input_filename</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">input_handle</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">alignments</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">AlignIO</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">parse</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">input_handle</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"fasta"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">sequence_names</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>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignment</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignments</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">any_modified_names</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">with</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">input_filename</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;">input_handle</span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">alignment</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">AlignIO</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">input_handle</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"fasta"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">sequence_names</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>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Remove disallowed characters</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'#'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'#'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span><span class="s" style="color: #d14;">"_"</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">":"</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="LC74" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_"</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_"</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_"</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">":"</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="LC76" class="line" lang="python"> <span class="n" style="color: #333;">any_modified_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Store modified names</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">sequence_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">[</span><span class="n" style="color: #333;">k</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">Counter</span><span class="p">(</span><span class="n" style="color: #333;">sequence_names</span><span class="p">).</span><span class="n" style="color: #333;">items</span><span class="p">())</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</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="p">[]:</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">input_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Update alignment if names changed</span></span>
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<pre style="margin: 0;">+<span id="LC82" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">,</span><span class="n" style="color: #333;">output_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> </span></pre>
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<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#aaaba74cad9a3f815206ba8bf91e26f24eb5a22a"><strong>python/gubbins/common.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">@@ -256,8 +256,9 @@ def parse_and_run(input_args, program_description=""):</td>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 3.5a. Joint ancestral reconstruction with new tree and info file in each iteration</span></span>
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">info_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_fitter</span><span class="p">.</span><span class="n" style="color: #333;">get_info_filename</span><span class="p">(</span><span class="n" style="color: #333;">temp_working_dir</span><span class="p">,</span><span class="n" style="color: #333;">current_basename</span><span class="p">)</span></span>
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258
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">recontree_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model_fitter</span><span class="p">.</span><span class="n" style="color: #333;">get_recontree_filename</span><span class="p">(</span><span class="n" style="color: #333;">temp_working_dir</span><span class="p">,</span><span class="n" style="color: #333;">current_basename</span><span class="p">)</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Arbitrary rooting of tree</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">reroot_tree_at_midpoint</span><span class="p">(</span><span class="n" style="color: #333;">recontree_filename</span><span class="p">)</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set root of reconstruction tree to match that of the current tree</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Cannot just midpoint root both, because the branch lengths differ between them</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">harmonise_roots</span><span class="p">(</span><span class="n" style="color: #333;">recontree_filename</span><span class="p">,</span> <span class="n" style="color: #333;">temp_rooted_tree</span><span class="p">)</span></span>
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261
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> </span>
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262
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">printer</span><span class="p">.</span><span class="k" style="font-weight: 600;">print</span><span class="p">([</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Running joint ancestral reconstruction with pyjar"</span><span class="p">])</span></span>
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263
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">jar</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">polymorphism_alignment</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># complete polymorphism alignment</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" 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="272" 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">@@ -271,8 +272,12 @@ def parse_and_run(input_args, program_description=""):</td>
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271
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_args</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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272
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">gaps_alignment_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp_working_dir</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;">ancestral_sequence_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".joint.aln"</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">raw_internal_rooted_tree_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp_working_dir</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;">ancestral_sequence_basename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".joint.tre"</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">transfer_internal_node_labels_to_tree</span><span class="p">(</span><span class="n" style="color: #333;">raw_internal_rooted_tree_filename</span><span class="p">,</span> <span class="n" style="color: #333;">temp_rooted_tree</span><span class="p">,</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">current_tree_name_with_internal_nodes</span><span class="p">,</span> <span class="s" style="color: #d14;">"pyjar"</span><span class="p">)</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">printer</span><span class="p">.</span><span class="k" style="font-weight: 600;">print</span><span class="p">([</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Transferring pyjar results onto original recombination-corrected tree"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">transfer_internal_node_labels_to_tree</span><span class="p">(</span><span class="n" style="color: #333;">raw_internal_rooted_tree_filename</span><span class="p">,</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">temp_rooted_tree</span><span class="p">,</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">current_tree_name_with_internal_nodes</span><span class="p">,</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="s" style="color: #d14;">"pyjar"</span><span class="p">)</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">printer</span><span class="p">.</span><span class="k" style="font-weight: 600;">print</span><span class="p">([</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Done transfer"</span><span class="p">])</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" 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="314" 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">@@ -309,10 +314,12 @@ def parse_and_run(input_args, program_description=""):</td>
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309
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">current_tree_name_with_internal_nodes</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_reconstructor</span><span class="p">)</span></span>
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310
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">input_args</span><span class="p">.</span><span class="n" style="color: #333;">seq_recon</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"iqtree"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">input_args</span><span class="p">.</span><span class="n" style="color: #333;">seq_recon</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"raxmlng"</span><span class="p">:</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># IQtree returns an unrooted tree</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">temp_unrooted_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp_working_dir</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;">current_tree_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".unrooted"</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">unroot_tree</span><span class="p">(</span><span class="n" style="color: #333;">temp_rooted_tree</span><span class="p">,</span> <span class="n" style="color: #333;">temp_unrooted_tree</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">transfer_internal_node_labels_to_tree</span><span class="p">(</span><span class="n" style="color: #333;">raw_internal_rooted_tree_filename</span><span class="p">,</span> <span class="n" style="color: #333;">temp_unrooted_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">current_tree_name_with_internal_nodes</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_reconstructor</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">harmonise_roots</span><span class="p">(</span><span class="n" style="color: #333;">raw_internal_rooted_tree_filename</span><span class="p">,</span> <span class="n" style="color: #333;">temp_rooted_tree</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">transfer_internal_node_labels_to_tree</span><span class="p">(</span><span class="n" style="color: #333;">raw_internal_rooted_tree_filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">temp_rooted_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">current_tree_name_with_internal_nodes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">sequence_reconstructor</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">use_root</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="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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317
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognised sequence reconstruction command: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">input_args</span><span class="p">.</span><span class="n" style="color: #333;">seq_recon</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="699" 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="706" 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">@@ -699,7 +706,6 @@ def reroot_tree_with_outgroup(tree_name, outgroups):</td>
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699
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706
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<pre style="margin: 0;"> <span id="LC706" 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;">tree_name</span><span class="p">,</span> <span class="s" style="color: #d14;">'w+'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_file</span><span class="p">:</span></span>
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700
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">output_tree_string</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="python"></span>
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703
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reroot_tree_at_midpoint</span><span class="p">(</span><span class="n" style="color: #333;">tree_name</span><span class="p">):</span></span>
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704
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">tree_name</span><span class="p">,</span> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_underscores</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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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;">split_all_non_bi_nodes</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="718" 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="724" 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">@@ -718,6 +724,50 @@ def unroot_tree(input_filename, output_filename):</td>
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718
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724
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<pre style="margin: 0;"> <span id="LC724" 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;">output_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w+'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_file</span><span class="p">:</span></span>
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719
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">output_tree_string</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">harmonise_roots</span><span class="p">(</span><span class="n" style="color: #333;">new_tree_fn</span><span class="p">,</span> <span class="n" style="color: #333;">tree_for_root_fn</span><span class="p">):</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read in tree and get nodes adjacent to root</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python"> <span class="n" style="color: #333;">taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">TaxonNamespace</span><span class="p">()</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python"> <span class="n" style="color: #333;">tree_for_root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">tree_for_root_fn</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python"> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python"> <span class="n" style="color: #333;">preserve_underscores</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="LC733" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxa</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"force-rooted"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"> <span class="n" style="color: #333;">tree_for_root</span><span class="p">.</span><span class="n" style="color: #333;">encode_bipartitions</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="python"> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree_for_root</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="python"> <span class="n" style="color: #333;">root_adjacent_bipartitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">root_adjacent_node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">child_nodes</span><span class="p">():</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="python"> <span class="n" style="color: #333;">root_adjacent_bipartitions</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">root_adjacent_node</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">bipartition</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Now search the new tree for these nodes</span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python"> <span class="n" style="color: #333;">new_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">new_tree_fn</span><span class="p">,</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="python"> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"> <span class="n" style="color: #333;">preserve_underscores</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="LC744" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxa</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"force-rooted"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="python"> <span class="n" style="color: #333;">new_tree</span><span class="p">.</span><span class="n" style="color: #333;">encode_bipartitions</span><span class="p">()</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new_tree</span><span class="p">.</span><span class="n" style="color: #333;">preorder_node_iter</span><span class="p">():</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">bipartition</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">root_adjacent_bipartitions</span><span class="p">:</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="python"> <span class="n" style="color: #333;">half_branch_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">edge_length</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python"> <span class="n" style="color: #333;">new_tree</span><span class="p">.</span><span class="n" style="color: #333;">reroot_at_edge</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="python"> <span class="n" style="color: #333;">length1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">half_branch_length</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="python"> <span class="n" style="color: #333;">length2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">half_branch_length</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="python"> <span class="n" style="color: #333;">new_tree_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree_as_string</span><span class="p">(</span><span class="n" style="color: #333;">new_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="python"> <span class="n" style="color: #333;">suppress_internal</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="LC756" class="line" lang="python"> <span class="n" style="color: #333;">suppress_rooting</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="LC757" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check both trees are topologically identical</span></span>
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python"> <span class="n" style="color: #333;">missing_bipartitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">.</span><span class="n" style="color: #333;">treecompare</span><span class="p">.</span><span class="n" style="color: #333;">find_missing_bipartitions</span><span class="p">(</span><span class="n" style="color: #333;">tree_for_root</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="python"> <span class="n" style="color: #333;">new_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="python"> <span class="n" style="color: #333;">is_bipartitions_updated</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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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="python"> </span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_bipartitions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Bipartitions missing when transferring node label transfer: '</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;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_bipartitions</span><span class="p">]))</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="python"></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write output</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" 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;">new_tree_fn</span><span class="p">,</span> <span class="s" style="color: #d14;">'w+'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_file</span><span class="p">:</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">new_tree_string</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"></span>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_out_removed_taxa_from_tree</span><span class="p">(</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">output_filename</span><span class="p">,</span> <span class="n" style="color: #333;">taxa_removed</span><span class="p">):</span></span>
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_underscores</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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723
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">prune_taxa_with_labels</span><span class="p">(</span><span class="n" style="color: #333;">taxa_removed</span><span class="p">,</span> <span class="n" style="color: #333;">update_bipartitions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="791" 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="841" 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">@@ -791,32 +841,70 @@ def get_monophyletic_outgroup(tree_name, outgroups):</td>
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">transfer_internal_node_labels_to_tree</span><span class="p">(</span><span class="n" style="color: #333;">source_tree_filename</span><span class="p">,</span> <span class="n" style="color: #333;">destination_tree_filename</span><span class="p">,</span> <span class="n" style="color: #333;">output_tree_filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="python"> <span class="n" style="color: #333;">sequence_reconstructor</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python"> <span class="n" style="color: #333;">sequence_reconstructor</span><span class="p">,</span> <span class="n" style="color: #333;">use_root</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="LC845" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read source tree and extract node labels, to match with the ancestral sequence reconstruction</span></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;">source_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">source_tree_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_underscores</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="LC798" class="line" lang="python"> <span class="n" style="color: #333;">source_internal_node_labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python"> <span class="n" style="color: #333;">taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">TaxonNamespace</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="python"> <span class="n" style="color: #333;">source_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">source_tree_filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python"> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="python"> <span class="n" style="color: #333;">preserve_underscores</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="LC850" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxa</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'force-rooted'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="python"> <span class="n" style="color: #333;">source_tree</span><span class="p">.</span><span class="n" style="color: #333;">encode_bipartitions</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">source_internal_node_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">source_internal_node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">source_tree</span><span class="p">.</span><span class="n" style="color: #333;">internal_nodes</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="python"> <span class="n" style="color: #333;">node_bipartition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">bipartition</span></span>
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">source_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">label</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="python"> <span class="n" style="color: #333;">source_internal_node_<span class="idiff left">labels</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">source_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">label</span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">source_internal_node_<span class="idiff left">dict</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">node_bipartition</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">source_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">label</span></span>
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<pre style="margin: 0;"> <span id="LC858" 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="LC803" class="line" lang="python"> <span class="n" style="color: #333;">source_internal_node_labels</span><span class="p">.</span><span class="n" style="color: #333;">append</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="LC804" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">source_internal_node_dict</span><span class="p">[</span><span class="n" style="color: #333;">node_bipartition</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read original tree and add in the labels from the ancestral sequence reconstruction</span></span>
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="python"> <span class="n" style="color: #333;">destination_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">destination_tree_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_underscores</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="LC807" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">destination_internal_node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">internal_nodes</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_reconstructor</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'pyjar'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="python"> <span class="n" style="color: #333;">new_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">source_internal_node_labels</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC810" 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="LC811" class="line" lang="python"> <span class="n" style="color: #333;">new_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_reconstructor</span><span class="p">.</span><span class="n" style="color: #333;">replace_internal_node_label</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">source_internal_node_labels</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="python"> <span class="n" style="color: #333;">destination_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="python"> <span class="n" style="color: #333;">destination_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Taxon</span><span class="p">(</span><span class="n" style="color: #333;">new_label</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">destination_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">destination_tree_filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python"> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">preserve_underscores</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="LC864" class="line" lang="python"> <span class="n" style="color: #333;">taxon_namespace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">taxa</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'force-rooted'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="python"> <span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">encode_bipartitions</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> </span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check both trees are topologically identical</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="python"> <span class="n" style="color: #333;">missing_bipartitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">calculate</span><span class="p">.</span><span class="n" style="color: #333;">treecompare</span><span class="p">.</span><span class="n" style="color: #333;">find_missing_bipartitions</span><span class="p">(</span><span class="n" style="color: #333;">source_tree</span><span class="p">,</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="python"> <span class="n" style="color: #333;">destination_tree</span><span class="p">,</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="python"> <span class="n" style="color: #333;">is_bipartitions_updated</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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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_bipartitions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Bipartitions missing when transferring node label transfer: '</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;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_bipartitions</span><span class="p">]))</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python"> </span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python"> <span class="n" style="color: #333;">root_alternative</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">destination_internal_node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">internal_nodes</span><span class="p">():</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">destination_internal_node</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">use_root</span><span class="p">:</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="python"> <span class="n" style="color: #333;">node_bipartition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">destination_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">edge</span><span class="p">.</span><span class="n" style="color: #333;">bipartition</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_reconstructor</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'pyjar'</span><span class="p">:</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"> <span class="n" style="color: #333;">new_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source_internal_node_dict</span><span class="p">[</span><span class="n" style="color: #333;">node_bipartition</span><span class="p">]</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Unable to find bipartition '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">node_bipartition</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="python"> <span class="n" style="color: #333;">new_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence_reconstructor</span><span class="p">.</span><span class="n" style="color: #333;">replace_internal_node_label</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">source_internal_node_dict</span><span class="p">[</span><span class="n" style="color: #333;">node_bipartition</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="python"> <span class="n" style="color: #333;">destination_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="python"> <span class="n" style="color: #333;">destination_internal_node</span><span class="p">.</span><span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Taxon</span><span class="p">(</span><span class="n" style="color: #333;">new_label</span><span class="p">)</span></span>
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890
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># output final tree</span></span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="python"> <span class="n" style="color: #333;">output_tree_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree_as_string</span><span class="p">(</span><span class="n" style="color: #333;">destination_tree</span><span class="p">,</span> <span class="n" style="color: #333;">suppress_internal</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;">suppress_rooting</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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817
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<pre style="margin: 0;">-<span id="LC817" 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;">output_tree_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w+'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_file</span><span class="p">:</span></span>
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818
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">output_tree_string</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">use_root</span><span class="p">:</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="python"> <span class="n" style="color: #333;">alt_root_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">root_child_node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">child_nodes</span><span class="p">():</span></span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="python"> <span class="n" style="color: #333;">alt_root_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">root_child_node</span><span class="p">.</span><span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">label</span></span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="python"> <span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">taxon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Taxon</span><span class="p">(</span><span class="n" style="color: #333;">alt_root_name</span><span class="p">)</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="python"> <span class="n" style="color: #333;">destination_tree_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">destination_tree</span><span class="p">.</span><span class="n" style="color: #333;">as_string</span><span class="p">(</span><span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"newick"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="python"> <span class="n" style="color: #333;">suppress_rooting</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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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python"> <span class="n" style="color: #333;">unquoted_underscores</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="LC902" class="line" lang="python"> <span class="n" style="color: #333;">suppress_internal_node_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"'"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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819
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="python"></span>
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904
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<pre style="margin: 0;">+<span id="LC904" 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;">output_tree_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w+'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">output_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">destination_tree_string</span><span class="p">,</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="python"> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="python"></span>
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_internal_node_labels_from_tree</span><span class="p">(</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">output_filename</span><span class="p">):</span></span>
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_path</span><span class="p">(</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_underscores</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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<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#7fda0caa14793966c396bc00135eaa6633fb5b4f"><strong>python/gubbins/pyjar.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,7 @@ try:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">NumpyShared</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="p">.</span><span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'NumpyShared'</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">'name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'shape'</span><span class="p">,</span> <span class="s" style="color: #d14;">'dtype'</span><span class="p">))</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"This version of Gubbins requires the multiprocessing library and python v3.8 or higher for memory management</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">201</span></span><span class="p">)</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gubbins.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">generate_shared_mem_array</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,31 +31,38 @@ from gubbins.utils import generate_shared_mem_array</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_alignment</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">file_type</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</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="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: alignment file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" does not exist"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">202</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Trying to open file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" as "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file_type</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">alignmentObject</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">),</span> <span class="n" style="color: #333;">file_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" 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;">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;">aln_in</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">alignmentObject</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">aln_in</span><span class="p">,</span> <span class="n" style="color: #333;">file_type</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Alignment read successfully"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot open alignment file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" as "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">file_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">203</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">alignmentObject</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#Calculate Pij from Q matrix and branch length</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calculate_pij</span><span class="p">(</span><span class="n" style="color: #333;">branch_length</span><span class="p">,</span><span class="n" style="color: #333;">rate_matrix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">branch_length</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,],</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,],</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,],</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),],</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),],</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),],</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="s" style="color: #d14;">"-inf"</span><span class="p">),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,]])</span></span>
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<pre style="margin: 0;"> <span id="LC54" 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="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">linalg</span><span class="p">.</span><span class="n" style="color: #333;">expm</span><span class="p">(</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">multiply</span><span class="p">(</span><span class="n" style="color: #333;">branch_length</span><span class="p">,</span><span class="n" style="color: #333;">rate_matrix</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">linalg</span><span class="p">.</span><span class="n" style="color: #333;">expm</span><span class="p">(</span><span class="n" style="color: #333;">numpy</span><span class="p">.</span><span class="n" style="color: #333;">multiply</span><span class="p">(</span><span class="n" style="color: #333;">branch_length</span><span class="p">,</span><span class="n" style="color: #333;">rate_matrix</span><span class="p">)))</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># modified</span></span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#Read the tree file and root</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_tree</span><span class="p">(</span><span class="n" style="color: #333;">treefile</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">treefile</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: tree file does not exist"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">treefile</span><span class="p">,</span> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"newick"</span><span class="p">,</span> <span class="n" style="color: #333;">preserve_underscores</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"force-rooted"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">204</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">treefile</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"newick"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">preserve_underscores</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="LC65" class="line" lang="python"> <span class="n" style="color: #333;">rooting</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"force-rooted"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Read the RAxML info file to get rates and frequencies</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">@@ -63,11 +70,11 @@ def read_info(infofile, type = 'raxml'):</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">infofile</span><span class="p">):</span></span>
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65
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: model information file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">infofile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" does not exist"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">205</span></span><span class="p">)</span></span>
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67
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> </span>
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68
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'raxml'</span><span class="p">,</span> <span class="s" style="color: #d14;">'raxmlng'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iqtree'</span><span class="p">,</span><span class="s" style="color: #d14;">'fasttree'</span><span class="p">]:</span></span>
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69
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Only able to parse GTR-type models from raxml, iqtree or fasttree'</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">206</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> </span>
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72
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">6</span> <span class="c1" style="color: #998; font-style: italic;"># initialise rates</span></span>
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73
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span> <span class="c1" style="color: #998; font-style: italic;"># initialise frequencies</span></span>
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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>
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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">@@ -146,7 +153,7 @@ def read_info(infofile, type = 'raxml'):</td>
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146
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check frequencies and rates have been extracted correctly</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">or</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="p">:</span></span>
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148
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Problem with extracting model parameters - frequencies are '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' and rates are '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">207</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">r</span></span>
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<pre style="margin: 0;"> <span id="LC159" 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">@@ -239,7 +246,7 @@ def reconstruct_alignment_column(column_indices, tree = None, alignment_sequence</td>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Iterate over columns</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">column</span><span class="p">,</span><span class="n" style="color: #333;">base_pattern_columns_padded</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="p">,</span><span class="n" style="color: #333;">column_positions</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### TIMING</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">calc_time_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">process_time</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">@@ -285,6 +292,7 @@ def reconstruct_alignment_column(column_indices, tree = None, alignment_sequence</td>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#1b. Set for each amino acid i: Ly(i) = Pij(ty), where ty is the branch length between y and its father.</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">L</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">:</span> <span class="n" style="color: #333;">pij</span><span class="p">[</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">"A"</span><span class="p">]][</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">taxon</span><span class="p">]]],</span> <span class="s" style="color: #d14;">"C"</span><span class="p">:</span> <span class="n" style="color: #333;">pij</span><span class="p">[</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">"C"</span><span class="p">]][</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">taxon</span><span class="p">]]],</span> <span class="s" style="color: #d14;">"G"</span><span class="p">:</span> <span class="n" style="color: #333;">pij</span><span class="p">[</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">"G"</span><span class="p">]][</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">taxon</span><span class="p">]]],</span> <span class="s" style="color: #d14;">"T"</span><span class="p">:</span> <span class="n" style="color: #333;">pij</span><span class="p">[</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="s" style="color: #d14;">"T"</span><span class="p">]][</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">taxon</span><span class="p">]]]}</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC296" 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="LC297" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">:</span> <span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">:</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">:</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">:</span> <span class="s" style="color: #d14;">"T"</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">@@ -292,7 +300,7 @@ def reconstruct_alignment_column(column_indices, tree = None, alignment_sequence</td>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot find"</span><span class="p">,</span> <span class="n" style="color: #333;">taxon</span><span class="p">,</span> <span class="s" style="color: #d14;">"in base"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">208</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> </span>
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">L</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="327" 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="335" 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">@@ -327,7 +335,6 @@ def reconstruct_alignment_column(column_indices, tree = None, alignment_sequence</td>
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">child</span><span class="p">.</span><span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">end</span><span class="p">]</span></span>
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">columnbases</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">base_frequencies</span><span class="p">[</span><span class="n" style="color: #333;">base_matrix</span><span class="p">[</span><span class="n" style="color: #333;">end</span><span class="p">]])</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">c</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="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]:</span></span>
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">j</span></span>
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">C</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">end</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="339" 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="346" 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">@@ -339,7 +346,7 @@ def reconstruct_alignment_column(column_indices, tree = None, alignment_sequence</td>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">max_root_base_likelihood</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">root_base</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">max_root_base</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">C</span><span class="p">[</span><span class="n" style="color: #333;">root_base</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_root_base</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Traverse the tree from the root in the direction of the OTUs, assigning to each node its most likely ancestral character as follows:</span></span>
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">node</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">preorder_node_iter</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC352" 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">@@ -354,8 +361,6 @@ def reconstruct_alignment_column(column_indices, tree = None, alignment_sequence</td>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">rootlens</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">child</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">child_node_iter</span><span class="p">():</span></span>
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356
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">rootlens</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">child</span><span class="p">.</span><span class="n" style="color: #333;">edge_length</span><span class="p">,</span><span class="n" style="color: #333;">child</span><span class="p">,</span><span class="n" style="color: #333;">child</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">rootlens</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><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;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">seed_node</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rootlens</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="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">r</span></span>
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364
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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;">### TIMING</span></span>
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="485" 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">@@ -480,7 +485,7 @@ def jar(alignment = None, base_patterns = None, base_pattern_positions = None, t</td>
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480
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485
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">taxon</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">taxon_namespace</span><span class="p">.</span><span class="n" style="color: #333;">get_taxon</span><span class="p">(</span><span class="n" style="color: #333;">nodename</span><span class="p">)</span></span>
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481
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486
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nodename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment_sequence_names</span><span class="p">:</span></span>
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482
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">nodename</span><span class="p">,</span> <span class="s" style="color: #d14;">"already in alignment. Quitting"</span><span class="p">)</span></span>
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483
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">209</span></span><span class="p">)</span></span>
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484
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">ancestral_node_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">nodename</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># index for reconstruction</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">parent_node</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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486
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">pij</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">calculate_pij</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">edge_length</span><span class="p">,</span> <span class="n" style="color: #333;">rm</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="558" 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">@@ -553,10 +558,17 @@ def jar(alignment = None, base_patterns = None, base_pattern_positions = None, t</td>
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553
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print tree</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gubbins.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tree_as_string</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Printing tree with internal nodes labelled: "</span><span class="p">,</span> <span class="n" style="color: #333;">output_prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".joint.tre"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC565" 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;">output_prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".joint.tre"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tree_output</span><span class="p">:</span></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">as_string</span><span class="p">(</span><span class="n" style="color: #333;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"newick"</span><span class="p">,</span> <span class="n" style="color: #333;">suppress_rooting</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">unquoted_underscores</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">suppress_internal_node_labels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"'"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tree_output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">recon_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree_as_string</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"> <span class="n" style="color: #333;">suppress_rooting</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="LC569" class="line" lang="python"> <span class="n" style="color: #333;">suppress_internal</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="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">recon_tree</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">'</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="LC571" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree_output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Done"</span><span class="p">)</span></span></pre>
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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">@@ -19,6 +19,7 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">gubbins.__init__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">version</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gubbins.common</span></span>
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<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#b37728bccd07a22008bf25dd8e4521fc8d157087"><strong>python/gubbins/treebuilders.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">@@ -629,8 +629,7 @@ class RAxMLNG:</td>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">citation</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://doi.org/10.1093/bioinformatics/btz305"</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set parallelisation</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</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="LC633" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"--threads"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"--threads"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add model</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"-model"</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">@@ -706,6 +705,7 @@ class RAxMLNG:</td>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">convert_raw_ancestral_states_to_fasta</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">output_filename</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python"> <span class="s" style="color: #d14;">"""Converts the file containing ancestral sequences into FASTA format"""</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use the IUPAC codes from here: https://www.bioinformatics.org/sms/iupac.html</span></span>
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<pre style="margin: 0;"> <span id="LC709" 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;">input_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;">infile</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC710" 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;">output_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">'w+'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outfile</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sequence_line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">infile</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">@@ -714,7 +714,13 @@ class RAxMLNG:</td>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python"> <span class="s" style="color: #d14;">'R'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"> <span class="s" style="color: #d14;">'Y'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="s" style="color: #d14;">'S'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"> <span class="s" style="color: #d14;">'W'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python"> <span class="s" style="color: #d14;">'W'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"> <span class="s" style="color: #d14;">'K'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python"> <span class="s" style="color: #d14;">'M'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"> <span class="s" style="color: #d14;">'B'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> <span class="s" style="color: #d14;">'D'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python"> <span class="s" style="color: #d14;">'H'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python"> <span class="s" style="color: #d14;">'V'</span><span class="p">:</span> <span class="s" style="color: #d14;">'N'</span></span>
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"> <span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#0452b1f8c4d2a44bb544f6ac29fc88719de5614e"><strong>python/gubbins/utils.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,18 +108,18 @@ def choose_executable_based_on_processor(list_of_executables: list):</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">).</span><span class="n" style="color: #333;">communicate</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">].</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="LC110" class="line" lang="python"> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cpu_info</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;"># Iterate through list to match with CPU features</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">list_of_executables</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">if</span></span> <span class="s" style="color: #d14;">'AVX2'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'avx2'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">flags</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="n" style="color: #333;">executable</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">break</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'AVX'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'avx'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">flags</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="n" style="color: #333;">executable</span><span class="p">):</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">break</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'SSE3'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'sse3'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">flags</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="n" style="color: #333;">executable</span><span class="p">):</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">break</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="p"><span class="idiff right">:</span></span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># Final executable on list is generic</span></span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">executable</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">list_of_executables</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span></span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Iterate through list to match with CPU features</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">list_of_executables</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cpu_info</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">and</span></span> <span class="s" style="color: #d14;">'AVX2'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'avx2'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">flags</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="n" style="color: #333;">executable</span><span class="p">):</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cpu_info</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">and</span></span> <span class="s" style="color: #d14;">'AVX'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'avx'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">flags</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="n" style="color: #333;">executable</span><span class="p">):</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cpu_info</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">and</span></span> <span class="s" style="color: #d14;">'SSE3'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executable</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'sse3'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">flags</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="n" style="color: #333;">executable</span><span class="p">):</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># to enable selection of raxml-ng-mpi</span></span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">elif</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'-mpi'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">executable</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">which</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">executable</span></span><span class="p"><span class="idiff right">):</span></span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">break</span></span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></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;"># Check executable is available</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="n" style="color: #333;">executable</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#364cbe5725a887b7cfe83f41addc60bf817a431d"><strong>python/scripts/extract_clade.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># encoding: utf-8</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Wellcome Trust Sanger Institute and Imperial College London</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (C) 2020 Wellcome Trust Sanger Institute and Imperial College London</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This program is free software; you can redistribute it and/or</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># modify it under the terms of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># as published by the Free Software Foundation; either version 2</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># of the License, or (at your option) any later version.</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># along with this program; if not, write to the Free Software</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Generic imports</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Phylogenetic imports</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dendropy</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Biopython imports</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AlignIO</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Phylo</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># command line parsing</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_options</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Mask recombinant regions detected by'</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">' Gubbins from the input alignment'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'mask_gubbins_aln'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># input options</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--list'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'List of sequences to extract'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--aln'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Input alignment (FASTA format)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--gff'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GFF of recombinant regions detected by Gubbins'</span><span class="p">,</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--tree'</span><span class="p">,</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Final tree generated by Gubbins'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--out'</span><span class="p">,</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Output file prefix'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--out-fmt'</span><span class="p">,</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Format of output alignment'</span><span class="p">,</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--missing-char'</span><span class="p">,</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Character used to replace recombinant sequence'</span><span class="p">,</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># main code</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get command line options</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_options</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse list of input sequences</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">subset</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read in FASTA assemblies</span></span>
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<pre style="margin: 0;">+<span id="LC74" 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;">args</span><span class="p">.</span><span class="nb" style="color: #0086b3;">list</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;">seq_list</span><span class="p">:</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" 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;">seq_list</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">():</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">subset</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Extract from alignment</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">output_aln_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.aln'</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">names_in_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" 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;">output_aln_name</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out_aln</span><span class="p">:</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">aln</span><span class="p">,</span><span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">taxon</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">names_in_alignment</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">subset</span><span class="p">:</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">,</span> <span class="n" style="color: #333;">out_aln</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out_fmt</span><span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check subset sequences are found in alignment</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">not_found_in_dataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subset</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">names_in_alignment</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">not_found_in_dataset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Sequences in subset missing from alignment: '</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">not_found_in_dataset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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="LC94" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Prune from the tree</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">output_tree_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tree'</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">,</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">schema</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'newick'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">preserve_underscores</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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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">retain_taxa_with_labels</span><span class="p">(</span><span class="n" style="color: #333;">subset</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">write_to_path</span><span class="p">(</span><span class="n" style="color: #333;">output_tree_name</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">'newick'</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Identify relevant recombination blocks</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">output_gff_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.gff'</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">taxon_pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'taxa="([^"]*)"'</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="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;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</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;">in_gff</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">output_gff_name</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out_gff</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" 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;">in_gff</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</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>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">out_gff</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">taxon_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">taxon_pattern</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]).</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">())</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">taxon_set</span><span class="p">.</span><span class="n" style="color: #333;">isdisjoint</span><span class="p">(</span><span class="n" style="color: #333;">subset</span><span class="p">):</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">out_gff</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span></pre>
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<li id="736ae1bee457a1fb132cee635e1205a31bf0f0a5">
<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#736ae1bee457a1fb132cee635e1205a31bf0f0a5"><strong>python/scripts/generate_ska_alignment.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># encoding: utf-8</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Wellcome Trust Sanger Institute and Imperial College London</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (C) 2020 Imperial College London and Imperial College London</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This program is free software; you can redistribute it and/or</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># modify it under the terms of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># as published by the Free Software Foundation; either version 2</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># of the License, or (at your option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># GNU General Public License for more details.</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># along with this program; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Generic imports</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Pool</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">functools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">partial</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">shutil</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">which</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># command line parsing</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_options</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Generate a ska alignment from a list '</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'of assemblies'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'generate_ska_alignment'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># input options</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--reference'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Name of reference sequence to use for alignment'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'List of FASTA files to include in alignment'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--fastq'</span><span class="p">,</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'List of FASTQ files to include in alignment'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--out'</span><span class="p">,</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Name of output alignment'</span><span class="p">,</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--k'</span><span class="p">,</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Split kmer size'</span><span class="p">,</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--threads'</span><span class="p">,</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Number of threads to use'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">default</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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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--no-cleanup'</span><span class="p">,</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Do not remove intermediate files'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">default</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="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">map_fasta_sequence</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">k</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;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span><span class="s" style="color: #d14;">'ska fasta -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">seq</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' -k '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">)</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;">seq</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">shell</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="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">map_fastq_sequence</span><span class="p">(</span><span class="n" style="color: #333;">read_pair</span><span class="p">,</span> <span class="n" style="color: #333;">k</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;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span><span class="s" style="color: #d14;">'ska fastq -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">read_pair</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' -k '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">)</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>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">read_pair</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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;">read_pair</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="LC73" class="line" lang="python"> <span class="n" style="color: #333;">shell</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="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ska_map_sequences</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">k</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;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span><span class="s" style="color: #d14;">'ska map -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.map -k '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' -r '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.skf'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">shell</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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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># main code</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get command line options</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_options</span><span class="p">()</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if ska is installed</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="s" style="color: #d14;">'ska'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'SKA cannot be found on PATH; install with "conda install ska"'</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Dictionary for sequence names</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">seq_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">all_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make split kmers from assemblies</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">fasta_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read in FASTA assemblies</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">fasta</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;">fasta_list</span><span class="p">:</span></span>
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100
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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;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_list</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">():</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">info</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="LC103" class="line" lang="python"> <span class="n" style="color: #333;">fasta_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">seq_names</span><span class="p">[</span><span class="n" style="color: #333;">info</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;">info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">all_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Unable to find file '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info</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="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sketch into split kmers</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Pool</span><span class="p">(</span><span class="n" style="color: #333;">processes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pool</span><span class="p">:</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">map_fasta_sequence</span><span class="p">,</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_names</span><span class="p">),</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">fasta_names</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> </span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make split kmers from FASTQs</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">fastq_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fastq</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read in FASTQ reads</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fastq</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;">fastq_list</span><span class="p">:</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="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;">fastq_list</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">():</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">fns</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">fns</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]):</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">fastq_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">seq_names</span><span class="p">[</span><span class="n" style="color: #333;">info</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;">info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">all_names</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Unable to find files '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fns</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="s" style="color: #d14;">' and '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fns</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sketch into split kmers</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Pool</span><span class="p">(</span><span class="n" style="color: #333;">processes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pool</span><span class="p">:</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">return_codes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">map_fastq_sequence</span><span class="p">,</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_names</span><span class="p">),</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">fastq_names</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Map sequences</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Pool</span><span class="p">(</span><span class="n" style="color: #333;">processes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pool</span><span class="p">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">return_codes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">ska_map_sequences</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">reference</span><span class="p">),</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">all_names</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Generate alignment</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span><span class="s" style="color: #d14;">'cat '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.map.aln'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_names</span><span class="p">])</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</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;">shell</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="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Clean up</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">no_cleanup</span><span class="p">:</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span><span class="s" style="color: #d14;">'rm '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.map.aln'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_names</span><span class="p">]),</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">shell</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span><span class="s" style="color: #d14;">'rm '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.skf'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_names</span><span class="p">]),</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">shell</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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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/gubbins/-/commit/099d39347d036549525167aafc660bc8b80a1bb3#73997306d4f22caca12478c8d6748a2653289fe5"><strong>python/scripts/mask_gubbins_aln.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># encoding: utf-8</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Wellcome Trust Sanger Institute and Imperial College London</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (C) 2020 Wellcome Trust Sanger Institute and Imperial College London</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This program is free software; you can redistribute it and/or</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># modify it under the terms of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># as published by the Free Software Foundation; either version 2</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># of the License, or (at your option) any later version.</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># along with this program; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Generic imports</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Biopython imports</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AlignIO</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Phylo</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># command line parsing</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_options</span><span class="p">():</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Mask recombinant regions detected by'</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">' Gubbins from the input alignment'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'mask_gubbins_aln'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># input options</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--aln'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Input alignment (FASTA format)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--gff'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GFF of recombinant regions detected by Gubbins'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--out'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Output file name'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--out-fmt'</span><span class="p">,</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Format of output alignment'</span><span class="p">,</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--missing-char'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Character used to replace recombinant sequence'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># main code</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get command line options</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_options</span><span class="p">()</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read in alignment</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">overall_taxon_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">aln</span><span class="p">,</span><span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">taxon</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment</span><span class="p">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">overall_taxon_list</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">tomutable</span><span class="p">()</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">overall_taxon_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">overall_taxon_list</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read recombinant regions from GFF</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">taxon_pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'taxa="([^"]*)"'</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</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;">gff_file</span><span class="p">:</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" 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;">gff_file</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">():</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">.</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>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</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>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">start</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;">info</span><span class="p">[</span><span class="mi" style="color: #099;">3</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="LC78" class="line" lang="python"> <span class="n" style="color: #333;">end</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;">info</span><span class="p">[</span><span class="mi" style="color: #099;">4</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="LC79" class="line" lang="python"> <span class="n" style="color: #333;">taxon_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">taxon_pattern</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]).</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon_set</span><span class="p">.</span><span class="n" style="color: #333;">issubset</span><span class="p">(</span><span class="n" style="color: #333;">overall_taxon_set</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">taxon</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">taxon_set</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">taxon</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">end</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">missing_char</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start</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="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write out masked sequence</span></span>
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<pre style="margin: 0;">+<span id="LC86" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out_aln</span><span class="p">:</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">AlignIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="n" style="color: #333;">out_aln</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out_fmt</span><span class="p">)</span></span></pre>
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