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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/metaphlan2">Debian Med / metaphlan2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478">f3802d9f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T19:15:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.14</pre>
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<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7b846cc7b993e3bf9c89f934f3dc2fd2da05f7a3">
metaphlan/metaphlan.py
</a>
</li>
<li class="file-stats">
<a href="#7aafae8111714ffa2e2a8985a5551b6f2b1540ce">
metaphlan/strainphlan.py
</a>
</li>
<li class="file-stats">
<a href="#cfa017e7bfc546ca60143211aa843dea75982f85">
metaphlan/utils/calculate_unifrac.R
</a>
</li>
<li class="file-stats">
<a href="#88d648f97455ad241b6c1301829e22a15b1c3668">
metaphlan/utils/external_exec.py
</a>
</li>
<li class="file-stats">
<a href="#f15e9945fd3f058fb95b4a50aaac9736c1af18ca">
metaphlan/utils/extract_markers.py
</a>
</li>
<li class="file-stats">
<a href="#9b77fa2753ec76dd4bc13c02c2b9112b1c91737e">
metaphlan/utils/merge_metaphlan_tables.py
</a>
</li>
<li class="file-stats">
<a href="#db8470d3c11d4d5435be70c3bf5bd93699520a57">
metaphlan/utils/sample2markers.py
</a>
</li>
<li class="file-stats">
<a href="#805b05166d70d8a1fa10f5aea0ace810e0754c58">
metaphlan/utils/strain_transmission.py
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7b846cc7b993e3bf9c89f934f3dc2fd2da05f7a3">
<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#7b846cc7b993e3bf9c89f934f3dc2fd2da05f7a3"><strong>metaphlan/metaphlan.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">@@ -4,8 +4,8 @@ __author__ = ('Francesco Beghini (francesco.beghini@unitn.it),'</td>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="s" style="color: #d14;">'Duy Tin Truong, '</span></span>
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Asnicar (f.asnicar@unitn.it), '</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="s" style="color: #d14;">'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">3</span>'</span></span>
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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">27 Jul</span> 202<span class="idiff right">1</span>'</span></span>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">19 Jan</span> 202<span class="idiff right">2</span>'</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="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="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<li id="7aafae8111714ffa2e2a8985a5551b6f2b1540ce">
<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#7aafae8111714ffa2e2a8985a5551b6f2b1540ce"><strong>metaphlan/strainphlan.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">@@ -4,8 +4,8 @@ __author__ = ('Aitor Blanco Miguez (aitor.blancomiguez@unitn.it), '</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Asnicar (f.asnicar@unitn.it), '</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">'Moreno Zolfo (moreno.zolfo@unitn.it), '</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Beghini (francesco.beghini@unitn.it)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">3</span>'</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">27 Jul</span> 202<span class="idiff right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">19 Jan</span> 202<span class="idiff right">2</span>'</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>
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<pre style="margin: 0;"> <span id="LC11" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ if sys.version_info[0] < 3:</td>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> </span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">exit</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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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></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;">os</span><span class="p">,</span> <span class="n" style="color: #333;">pickle</span><span class="p">,</span> <span class="n" style="color: #333;">time</span><span class="p">,</span> <span class="n" style="color: #333;">bz2</span><span class="p">,</span> <span class="n" style="color: #333;">numpy</span><span class="p">,</span> <span class="n" style="color: #333;">collections</span><span class="p">,</span> <span class="n" style="color: #333;">tempfile</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;">os</span><span class="p">,</span> <span class="n" style="color: #333;">pickle</span><span class="p">,</span> <span class="n" style="color: #333;">time</span><span class="p">,</span> <span class="n" style="color: #333;">bz2</span><span class="p">,</span> <span class="n" style="color: #333;">numpy</span><span class="p">,</span> <span class="n" style="color: #333;">collections</span><span class="p">,</span> <span class="n" style="color: #333;">tempfile</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">shutil</span></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ap</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">shutil</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">copyfile</span><span class="p">,</span> <span class="n" style="color: #333;">rmtree</span><span class="p">,</span> <span class="n" style="color: #333;">move</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;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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">@@ -68,10 +68,12 @@ def read_params():</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The number of bases to remove from both ends when trimming markers"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--marker_in_n_samples'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">80</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC70" 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;">"Theshold defining the minimum percentage of samples to keep a marker"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sample_with_n_markers'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC72" 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;">"Threshold defining the minimun number of markers to keep a sample"</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;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--secondary_sample_with_n_markers'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Threshold defining the minimun number of markers to keep a secondary sample"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sample_with_n_markers'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">80</span><span class="p">,</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Threshold defining the minimun percentage of markers to keep a sample"</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;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--secondary_sample_with_n_markers'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">80</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" 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;">"Threshold defining the minimun percentage of markers to keep a secondary sample"</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;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--sample_with_n_markers_after_filt'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" 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;">"Threshold defining the minimun percentage of markers to keep a sample after filtering the markers [only for dev]"</span><span class="p">)</span></span>
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75
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<td class="new_line diff-line-num" data-linenumber="77" 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">
77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--phylophlan_mode'</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PHYLOPHLAN_MODES</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'fast'</span><span class="p">,</span></span>
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76
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<td class="new_line diff-line-num" data-linenumber="78" 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">
78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The presets for fast or accurate phylogenetic analysis"</span><span class="p">)</span></span>
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77
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<td class="new_line diff-line-num" data-linenumber="79" 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">
79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--phylophlan_configuration'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,6 +146,8 @@ def check_params(args):</td>
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144
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">init_new_line</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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145
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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;">print_clades_only</span> <span class="ow" style="font-weight: 600;">and</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;">output_dir</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">):</span></span>
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146
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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;">args</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'/'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" 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;">sample_with_n_markers</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">50</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample_with_n_markers_after_filt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample_with_n_markers</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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147
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>
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148
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">args</span></span>
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149
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" 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="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,7 +198,7 @@ def add_secondary_samples(secondary_samples, cleaned_markers_matrix,</td>
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194
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">markers_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">execute_pool</span><span class="p">(((</span><span class="n" style="color: #333;">get_matrix_for_sample</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">secondary_samples</span><span class="p">),</span> </span>
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195
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">nprocs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">markers_matrix</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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;">secondary_samples_with_n_markers</span><span class="p">:</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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 class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</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"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">values</span></span><span class="p"><span class="idiff">())[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:])</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">secondary_samples_with_n_markers</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)</span> </span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cleaned_markers_matrix</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">@@ -219,7 +223,7 @@ def add_secondary_references(secondary_references, cleaned_markers_matrix,</td>
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219
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">clade_markers_file</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">secondary_references</span><span class="p">),</span> </span>
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220
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">nprocs</span><span class="p">)</span></span>
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">markers_matrix</span><span class="p">:</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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;">secondary_samples_with_n_markers</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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 class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</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"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">values</span></span><span class="p"><span class="idiff">())[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:])</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">secondary_samples_with_n_markers</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)</span> </span>
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cleaned_markers_matrix</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="289" 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="293" 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">@@ -289,14 +293,15 @@ a threhold, if not, removes the marker.</td>
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289
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;"> samples to keep a marker</span></span>
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290
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;">:returns: the filtered markers matrix</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clean_markers_matrix</span><span class="p">(</span><span class="n" style="color: #333;">markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clean_markers_matrix</span><span class="p">(</span><span class="n" style="color: #333;">markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">sample_with_n_markers_after_filt</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">messages</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="LC298" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Checks if the percentage of markers of a sample sample reachs a threshold, </span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not, removes the sample </span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not, removes the sample </span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">total_markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">markers_matrix</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="LC301" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">markers_matrix</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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;">samples_with_n_markers</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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 class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</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"> </span><span class="n" style="color: #333;"><span class="idiff">total_markers</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">to_remove</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC306" 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="LC307" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">({</span><span class="s" style="color: #d14;">'sample'</span><span class="p">:</span> <span class="n" style="color: #333;">m</span><span class="p">[</span><span class="s" style="color: #d14;">'sample'</span><span class="p">]})</span> </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">@@ -309,7 +314,7 @@ def clean_markers_matrix(markers_matrix, samples_with_n_markers,</td>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Phylogeny can not be inferred. Too many samples were discarded"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</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;">init_new_line</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="LC316" 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="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">total_markers</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">(</span></span><span class="n" style="color: #333;"><span class="idiff">sample_with_n_markers_after_filt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Checks if the percentage of samples that contain a marker reachs a threhold,</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not, removes the marker</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">@@ -325,18 +330,18 @@ def clean_markers_matrix(markers_matrix, samples_with_n_markers,</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">counter</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="LC331" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Checks how many markers were deleted</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" 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="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">values</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;">samples_with_n_markers</span><span class="p">:</span> </span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">values</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 class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</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"> </span><span class="n" style="color: #333;"><span class="idiff">total_markers</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">:</span> </span>
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329
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">messages</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Phylogeny can not be inferred. Too many markers were discarded"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</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;">init_new_line</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="LC337" 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="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">total_markers</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">(</span></span><span class="n" style="color: #333;"><span class="idiff">sample_with_n_markers_after_filt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Checks again if the percentage of markers of a sample sample is at least 1, </span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not, removes the sample </span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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 class="idiff left"><</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">values</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 class="idiff">*</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</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"> </span><span class="n" style="color: #333;"><span class="idiff">total_markers</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 right">sample_with_n_markers_after_filt</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">to_remove</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">to_remove</span><span class="p">:</span></span>
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="352" 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">@@ -347,9 +352,9 @@ def clean_markers_matrix(markers_matrix, samples_with_n_markers,</td>
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Phylogeny can not be inferred. No enough markers were kept for the samples"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</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;">init_new_line</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="LC354" 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="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">total_markers</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">(</span></span><span class="n" style="color: #333;"><span class="idiff">sample_with_n_markers_after_filt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cleaned_markers_matrix</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">total_markers</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">(</span></span><span class="n" style="color: #333;"><span class="idiff">sample_with_n_markers_after_filt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="415" 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">@@ -410,7 +415,7 @@ def sample_markers_to_fasta(sample_path, filtered_samples, tmp_dir, filtered_cla</td>
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sample</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="p">[</span><span class="s" style="color: #d14;">'marker'</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filtered_clade_markers</span><span class="p">:</span></span>
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412
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">marker_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_marker_name</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="s" style="color: #d14;">'marker'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence'</span><span class="p">][</span><span class="n" style="color: #333;">trim_sequences</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">trim_sequences</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 class="idiff left">N"</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">replace</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-"</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff">"N"</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">'N'</span></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;">marker_name</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;">marker_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence'</span><span class="p">][</span><span class="n" style="color: #333;">trim_sequences</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">trim_sequences</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 class="idiff left right">-"</span></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;">marker_name</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;">marker_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC419" 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;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">marker_fna</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="LC420" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC421" 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">@@ -421,8 +426,9 @@ Writes a FASTA file with the sequences of the filtered clade markers</td>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"><span class="s" style="color: #d14;">:param tmp_dir: the output temporal directory</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"><span class="s" style="color: #d14;">:param clade: the threads used for execution</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"><span class="s" style="color: #d14;">:param clade_markers_file: the FASTA with the clade markers</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"><span class="s" style="color: #d14;">:param trim_sequences: the number of bases to remove when trimming markers</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleaned_clade_markers_to_fasta</span><span class="p">(</span><span class="n" style="color: #333;">markers</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleaned_clade_markers_to_fasta</span><span class="p">(</span><span class="n" style="color: #333;">markers</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers_file</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trim_sequences</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmp_dir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clade</span><span class="p">[:</span><span class="mi" style="color: #099;">30</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="LC433" class="line" lang="python"> <span class="n" style="color: #333;">create_folder</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC434" 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">@@ -433,7 +439,7 @@ def cleaned_clade_markers_to_fasta(markers, tmp_dir, clade, clade_markers_file):</td>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</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;">markers</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="LC440" class="line" lang="python"> <span class="n" style="color: #333;">marker_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_marker_name</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC441" 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;">tmp_dir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">marker_name</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.fna'</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;">marker_fna</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">clade_markers</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">m</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;">marker_name</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;">marker_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">clade_markers</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">)<span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">trim_sequences</span></span><span class="p"><span class="idiff">:</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">trim_sequences</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">marker_name</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;">marker_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC443" 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;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">marker_fna</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="LC444" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC445" 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">@@ -540,6 +546,7 @@ def get_phylophlan_configuration():</td>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"><span class="s" style="color: #d14;">Executes PhyloPhlAn2 to compute phylogeny</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"><span class="s" style="color: #d14;">:param samples_list: the list of the primary and secondary metagenomic samples</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"><span class="s" style="color: #d14;">:param samples_markers_dir: the temporal samples markers directory</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"><span class="s" style="color: #d14;">:param num_samples: the number of filtered samples</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"><span class="s" style="color: #d14;">:param tmp_dir: the temporal output directory</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">@@ -551,8 +558,8 @@ Executes PhyloPhlAn2 to compute phylogeny</td>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"><span class="s" style="color: #d14;">:param mutation_rates: whether get the mutation rates for the markers</span></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"><span class="s" style="color: #d14;">:param nproc: the number of threads to run phylophlan</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">compute_phylogeny</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">num_samples</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="python"> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span> <span class="n" style="color: #333;">mutation_rates</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">):</span> </span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">compute_phylogeny</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">samples_list</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">num_samples</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">min_markers</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span> <span class="n" style="color: #333;">mutation_rates</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">):</span> </span>
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556
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"> <span class="n" style="color: #333;">info</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;">Creating PhyloPhlAn 3.0 database..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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557
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="n" style="color: #333;">create_phylophlan_db</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">[:</span><span class="mi" style="color: #099;">30</span><span class="p">])</span></span>
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558
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">info</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;">Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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="561" 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="568" 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">@@ -561,9 +568,10 @@ def compute_phylogeny(samples_markers_dir, num_samples, tmp_dir, output_dir, cla</td>
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561
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <span class="n" style="color: #333;">conf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_phylophlan_configuration</span><span class="p">()</span></span>
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562
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">phylophlan_configuration</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">generate_phylophlan_config_file</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">conf</span><span class="p">)</span></span>
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563
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">info</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;">Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">fake_phylophlan_inputs</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">samples_list</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">)</span></span>
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564
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">info</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;">Processing samples..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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565
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">min_entries</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;">marker_in_n_samples</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_samples</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="python"> <span class="n" style="color: #333;">execute_phylophlan</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span> <span class="n" style="color: #333;">min_entries</span><span class="p">,</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">execute_phylophlan</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span> <span class="n" style="color: #333;">min_entries</span><span class="p">,</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">round</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">min_markers</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)),</span></span></span>
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567
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> <span class="n" style="color: #333;">mutation_rates</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">)</span></span>
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568
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mutation_rates</span><span class="p">:</span></span>
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569
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"mutation_rates.tsv"</span><span class="p">,</span><span class="n" style="color: #333;">output_dir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".mutation"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="571" 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="579" 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">@@ -571,6 +579,31 @@ def compute_phylogeny(samples_markers_dir, num_samples, tmp_dir, output_dir, cla</td>
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571
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">info</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;">Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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572
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"></span>
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573
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"><span class="s" style="color: #d14;">Fakes the PhyloPhlAn inputs for the reconstructed markers</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"><span class="s" style="color: #d14;">:param output_dir: the output_directory</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"><span class="s" style="color: #d14;">:param samples_list: the list of the primary and secondary metagenomic samples</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"><span class="s" style="color: #d14;">:param tmp_dir: the temporal output directory</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"><span class="s" style="color: #d14;">:param samples_markers_dir: the temporal samples markers directory</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"><span class="s" style="color: #d14;">:param clade: the clade</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fake_phylophlan_inputs</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">samples_list</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">s</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="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'.pkl'</span><span class="p">,</span><span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples_list</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'markers_dna'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'map_dna'</span><span class="p">))</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'clean_dna'</span><span class="p">))</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">):</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'.fna'</span><span class="p">,</span><span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'map_dna'</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'.fna'</span><span class="p">,</span><span class="s" style="color: #d14;">'.b6o.bkp'</span><span class="p">)),</span> <span class="s" style="color: #d14;">'a'</span><span class="p">).</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'map_dna'</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'.fna'</span><span class="p">,</span><span class="s" style="color: #d14;">'.b6o.bz2'</span><span class="p">)),</span> <span class="s" style="color: #d14;">'a'</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="LC600" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">),</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'clean_dna'</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="p">))</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">bz2</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'markers_dna'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{}.bz2'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">)),</span> <span class="s" style="color: #d14;">'wt'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">write_file</span><span class="p">:</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" 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;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">sample</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;">read_file</span><span class="p">:</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" 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;">read_file</span><span class="p">:</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">write_file</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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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"></span>
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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575
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python"><span class="s" style="color: #d14;">Generates a file with the polimorfic rates of the species for each sample</span></span>
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576
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="654" 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="687" 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">@@ -654,8 +687,8 @@ def write_info(cleaned_markers_matrix, num_markers_for_clade, clade, output_dir,</td>
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654
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687
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Number of available markers for the clade: "</span> <span class="o" style="font-weight: 600;">+</span> </span>
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655
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688
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">num_markers_for_clade</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;">Filtering parameters: "</span> <span class="o" style="font-weight: 600;">+</span></span>
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656
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689
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Number of bases to remove when trimming markers: "</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;">trim_sequences</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Minimun <span class="idiff left right">number</span> of markers to keep a main sample: "</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;">samples_with_n_markers</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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658
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Minimun <span class="idiff left right">number</span> of markers to keep a secondary sample: "</span> <span class="o" style="font-weight: 600;">+</span> </span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Minimun <span class="idiff left right">percentage</span> of markers to keep a main sample: "</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;">samples_with_n_markers</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Minimun <span class="idiff left right">percentage</span> of markers to keep a secondary sample: "</span> <span class="o" style="font-weight: 600;">+</span> </span>
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659
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">secondary_samples_with_n_markers</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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660
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693
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Minimum percentage of samples to keep a marker: "</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;">marker_in_n_samples</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Number of markers selected after filtering: "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">())</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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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">@@ -678,7 +711,7 @@ Prints the clades detected in the reconstructed markers</td>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"><span class="s" style="color: #d14;">:param marker_in_n_samples: threshold defining the minimum percentage of samples</span></span>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"><span class="s" style="color: #d14;"> to keep a marker</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_clades</span><span class="p">(</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_clades</span><span class="p">(</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">sample_with_n_markers_after_filt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"> <span class="n" style="color: #333;">sample_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="n" style="color: #333;">markers2species</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"> <span class="n" style="color: #333;">species2markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<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 +747,7 @@ def print_clades(database, samples, samples_with_n_markers, marker_in_n_samples)</td>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="python"> <span class="n" style="color: #333;">species_markers_matrix</span><span class="p">[</span><span class="n" style="color: #333;">species</span><span class="p">][</span><span class="n" style="color: #333;">sample_id</span><span class="p">][</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="s" style="color: #d14;">'marker'</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="LC748" class="line" lang="python"> <span class="n" style="color: #333;">sample_id</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="LC749" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">species</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">species_markers_matrix</span><span class="p">:</span> </span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clean_markers_matrix</span><span class="p">(</span><span class="n" style="color: #333;">species_markers_matrix</span><span class="p">[</span><span class="n" style="color: #333;">species</span><span class="p">],</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clean_markers_matrix</span><span class="p">(</span><span class="n" style="color: #333;">species_markers_matrix</span><span class="p">[</span><span class="n" style="color: #333;">species</span><span class="p">],</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">sample_with_n_markers_after_filt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC751" 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;">cleaned_markers_matrix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</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;">species2samples</span><span class="p">[</span><span class="n" style="color: #333;">species</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Done.'</span><span class="p">,</span><span class="n" style="color: #333;">init_new_line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -756,10 +789,10 @@ Executes StrainPhlAn</td>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">strainphlan</span><span class="p">(</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">secondary_samples</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="n" style="color: #333;">secondary_references</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">trim_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="python"> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">secondary_samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="python"> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">secondary_samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">sample_with_n_markers_after_filt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> </span>
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"> <span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">mutation_rates</span><span class="p">,</span> <span class="n" style="color: #333;">print_clades_only</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">print_clades_only</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="python"> <span class="n" style="color: #333;">print_clades</span><span class="p">(</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">print_clades</span><span class="p">(</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">sample_with_n_markers_after_filt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC796" 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="LC797" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Creating temporary directory..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">mkdtemp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_dir</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tmp</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">mkdtemp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmp</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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="806" 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">@@ -773,8 +806,8 @@ def strainphlan(database, clade_markers, samples, references, secondary_samples,</td>
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python"> <span class="n" style="color: #333;">markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">)</span></span>
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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="LC808" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Removing bad markers / samples..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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="LC776" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clean_markers_matrix</span><span class="p">(</span><span class="n" style="color: #333;">markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="python"> <span class="n" style="color: #333;">marker_in_n_samples</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;">cleaned_markers_matrix</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">min_markers</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clean_markers_matrix</span><span class="p">(</span><span class="n" style="color: #333;">markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">samples_with_n_markers</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">sample_with_n_markers_after_filt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">)</span></span>
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778
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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779
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_markers_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_secondary_samples_and_references</span><span class="p">(</span><span class="n" style="color: #333;">secondary_samples</span><span class="p">,</span> </span>
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780
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"> <span class="n" style="color: #333;">secondary_references</span><span class="p">,</span> <span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">secondary_samples_with_n_markers</span><span class="p">,</span> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="818" 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">@@ -785,15 +818,15 @@ def strainphlan(database, clade_markers, samples, references, secondary_samples,</td>
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785
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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;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">)</span></span>
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786
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<td class="new_line diff-line-num" data-linenumber="819" 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">
819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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787
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<td class="new_line diff-line-num" data-linenumber="820" 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">
820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Writing filtered clade markers as FASTA file..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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="old_line diff-line-num old" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
788
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<td class="new_line diff-line-num old" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_clade_markers_to_fasta</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers_file</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="821" 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">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="python"> <span class="n" style="color: #333;">cleaned_clade_markers_to_fasta</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers_file</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trim_sequences</span></span><span class="p">)</span></span>
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789
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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790
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Calculating polymorphic rates..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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791
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<td class="new_line diff-line-num" data-linenumber="824" 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">
824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="python"> <span class="n" style="color: #333;">num_markers_for_clade</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculate_polimorfic_rates</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">secondary_samples</span><span class="p">,</span> <span class="n" style="color: #333;">clade_markers_file</span><span class="p">,</span> </span>
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792
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="python"> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">)</span></span>
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793
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826
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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794
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Executing PhyloPhlAn 3.0..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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795
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">compute_phylogeny</span><span class="p">(</span><span class="n" style="color: #333;">samples_as_markers_dir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">),</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> </span>
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796
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="python"> <span class="n" style="color: #333;">compute_phylogeny</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">samples</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">secondary_samples</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">samples_as_markers_dir</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cleaned_markers_matrix</span><span class="p">),</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> </span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">min_markers</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> <span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span></span>
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797
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<td class="new_line diff-line-num" data-linenumber="830" 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">
830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">mutation_rates</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">)</span></span>
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798
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Done."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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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799
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Writing information file..."</span><span class="p">,</span> <span class="n" style="color: #333;">init_new_line</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 new_line" data-linenumber="875" 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">@@ -842,7 +875,7 @@ def main():</td>
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842
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="python"> <span class="n" style="color: #333;">strainphlan</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">database</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">clade_markers</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">references</span><span class="p">,</span> </span>
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843
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<td class="new_line diff-line-num" data-linenumber="876" 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">
876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">secondary_samples</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">secondary_references</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> </span>
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844
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<td class="new_line diff-line-num" data-linenumber="877" 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">
877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">trim_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">marker_in_n_samples</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
845
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<td class="new_line diff-line-num old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">secondary_sample_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span> </span>
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<td class="old_line diff-line-num new" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">secondary_sample_with_n_markers</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sample_with_n_markers_after_filt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">phylophlan_mode</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">phylophlan_configuration</span><span class="p">,</span> </span>
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846
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<td class="new_line diff-line-num" data-linenumber="879" 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">
879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mutation_rates</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">print_clades_only</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nprocs</span><span class="p">)</span></span>
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847
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="python"> <span class="n" style="color: #333;">exec_time</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;">time</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t0</span></span>
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<td class="old_line diff-line-num" data-linenumber="848" 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">
848
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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;">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;">print_clades_only</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#cfa017e7bfc546ca60143211aa843dea75982f85"><strong>metaphlan/utils/calculate_unifrac.R</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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="49" 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">@@ -49,6 +49,11 @@ mpa_table <- mpa_table[,-1]</td>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="r"><span class="n" style="color: #333;">mpa_tree</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ape</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read.tree</span><span class="p">(</span><span class="n" style="color: #333;">tree_file</span><span class="p">)</span></span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="r"><span class="n" style="color: #333;">mpa_tree</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">tip.label</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">gsub</span><span class="p">(</span><span class="s2" style="color: #d14;">".+\\|s__"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">""</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mpa_tree</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">tip.label</span><span class="p">)</span></span>
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51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="r"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="r"><span class="n" style="color: #333;">removed</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">setdiff</span><span class="p">(</span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">mpa_table</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mpa_tree</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">tip.label</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="r"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">length</span><span class="p">(</span><span class="n" style="color: #333;">removed</span><span class="p">)){</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">paste0</span><span class="p">(</span><span class="s1" style="color: #d14;">'WARNING: '</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">length</span><span class="p">(</span><span class="n" style="color: #333;">removed</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="s1" style="color: #d14;">' species not present in the tree were removed from the input profile.'</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">stdout</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">removed</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">colllapse</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'\n'</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">stdout</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="r"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="r"><span class="n" style="color: #333;">filt_tree</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ape</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">keep.tip</span><span class="p">(</span><span class="n" style="color: #333;">mpa_tree</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">intersect</span><span class="p">(</span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">mpa_table</span><span class="p">),</span><span class="n" style="color: #333;">mpa_tree</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">tip.label</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="r"><span class="n" style="color: #333;">filt_mpa_table</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mpa_table</span><span class="p">[</span><span class="n" style="color: #333;">filt_tree</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">tip.label</span><span class="p">,]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">/</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">100.0</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="r"></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#88d648f97455ad241b6c1301829e22a15b1c3668"><strong>metaphlan/utils/external_exec.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">@@ -135,7 +135,7 @@ Executes PhyloPhlAn</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="s" style="color: #d14;">:param mutation_rates: whether get the mutation rates for the markers</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;">:param nproc: the number of threads to run phylophlan</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">execute_phylophlan</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">conf_file</span><span class="p">,</span> <span class="n" style="color: #333;">min_entries</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">execute_phylophlan</span><span class="p">(</span><span class="n" style="color: #333;">samples_markers_dir</span><span class="p">,</span> <span class="n" style="color: #333;">conf_file</span><span class="p">,</span> <span class="n" style="color: #333;">min_entries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">min_markers</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">phylogeny_conf</span><span class="p">,</span> <span class="n" style="color: #333;">mutation_rates</span><span class="p">,</span> <span class="n" style="color: #333;">nprocs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">accuracy</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;">phylogeny_conf</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,7 +146,8 @@ def execute_phylophlan(samples_markers_dir, conf_file, min_entries, tmp_dir, out</td>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"params"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"-d "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clade</span><span class="p">[:</span><span class="mi" style="color: #099;">30</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" --data_folder "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tmp_dir</span><span class="o" style="font-weight: 600;">+</span></span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">" --databases_folder "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tmp_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -t n -f "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">conf_file</span><span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">" --diversity low"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">accuracy</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" --genome_extension fna"</span><span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">" --force_nucleotides --min_num_entries "</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;">min_entries</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">" --force_nucleotides --min_num_entries "</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;">min_entries</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">" --min_num_markers "</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;">min_markers</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="s" style="color: #d14;">"input"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"-i"</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 class="s" style="color: #d14;">"output_path"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"--output_folder"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">"output"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#f15e9945fd3f058fb95b4a50aaac9736c1af18ca"><strong>metaphlan/utils/extract_markers.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">@@ -4,8 +4,8 @@ __author__ = ('Aitor Blanco Miguez (aitor.blancomiguez@unitn.it), '</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Asnicar (f.asnicar@unitn.it), '</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">'Moreno Zolfo (moreno.zolfo@unitn.it), '</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Beghini (francesco.beghini@unitn.it)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">1</span>'</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">07 Jul</span> 202<span class="idiff right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">19 Jan</span> 202<span class="idiff right">2</span>'</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="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="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#9b77fa2753ec76dd4bc13c02c2b9112b1c91737e"><strong>metaphlan/utils/merge_metaphlan_tables.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">@@ -32,12 +32,14 @@ def merge( aaastrIn, ostm ):</td>
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<pre style="margin: 0;"> <span id="LC32" 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;">headers</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="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'#'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</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="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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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">index_col</span> <span class="o" style="font-weight: 600;">=</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="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">mpaVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</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;">'#mpa_v[0-9]{2,}_CHOCOPhlAn_[0-9]{0,}'</span><span class="p">).</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">mpaVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</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;">'#mpa_v[0-9]{2,}_CHOCOPhlAn<span class="idiff left right">\w*/{0,3}</span>_[0-9]{0,}'</span><span class="p">).</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">headers</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;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">mpaVersion</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">listmpaVersion</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">mpaVersion</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="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" 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="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'merge_metaphlan_tables found tables without a header including the database version. Exiting.</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="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">listmpaVersion</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'merge_metaphlan_tables found tables made with different versions of the MetaPhlAn<span class="idiff left">2</span> database.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Please re-run MetaPhlAn<span class="idiff right">2</span> with the same database.</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="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'merge_metaphlan_tables found tables made with different versions of the MetaPhlAn database.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Please re-run MetaPhlAn with the same database.</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="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">iIn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> </span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#db8470d3c11d4d5435be70c3bf5bd93699520a57"><strong>metaphlan/utils/sample2markers.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">@@ -4,8 +4,8 @@ __author__ = ('Aitor Blanco Miguez (aitor.blancomiguez@unitn.it), '</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Asnicar (f.asnicar@unitn.it), '</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">'Moreno Zolfo (moreno.zolfo@unitn.it), '</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Beghini (francesco.beghini@unitn.it)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">0</span>'</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left">5</span> J<span class="idiff">u</span>n 202<span class="idiff right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left">9</span> J<span class="idiff">a</span>n 202<span class="idiff right">2</span>'</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="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="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#805b05166d70d8a1fa10f5aea0ace810e0754c58"><strong>metaphlan/utils/strain_transmission.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Aitor Blanco (aitor.blancomiguez@unitn.it), '</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"> <span class="s" style="color: #d14;">'Mireia Valles-Colomer (mireia.vallescolomer@unitn.it)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">0</span>'</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left">5</span> J<span class="idiff">u</span>n 202<span class="idiff right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left">9</span> J<span class="idiff">a</span>n 202<span class="idiff right">2</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span> <span class="n" style="color: #333;">time</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ap</span></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/-/commit/f3802d9f2ee7a5e4493de7acf4794adaa576a478#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ if sys.version_info[0] < 3:</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">setuptools</span><span class="p">.</span><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'MetaPhlAn'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">3</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'3.0.1<span class="idiff left right">4</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Francesco Beghini'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'francesco.beghini@unitn.it'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'http://github.com/biobakery/MetaPhlAn/'</span><span class="p">,</span></span>
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