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<h3>
David Parsons pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcalm">Debian Med / bcalm</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bcalm/-/commit/678808d35b226d838621f782ef760c6ce5f9c97d">678808d3</a></strong>
<div>
<span>by David Parsons</span>
<i>at 2020-08-20T15:55:45+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bcalm/-/commit/81349d42b89623b54a6a4fd4b3a443348a8586e3">81349d42</a></strong>
<div>
<span>by David Parsons</span>
<i>at 2020-08-20T15:57:55+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.3</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/-/commit/e3608b160becaccdd7b069de9ff18ba5ecad5fa3">e3608b16</a></strong>
<div>
<span>by David Parsons</span>
<i>at 2020-08-20T15:57:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.2.3'
Update to upstream version '2.2.3'
with Debian dir 79d3cde47411d000efea5d665f6bcaef7e4dd751</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<a href="#1d03bbf095557f92ea6b6f914caa2d3bb64b1772">
bidirected-graphs-in-bcalm2/bidirected-graphs-in-bcalm2.md
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#a08e8d09cd4ef472df3d2d101176256178ed50b7">
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+
scripts/abundance_stats.py
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<h4>Changes:</h4>
<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/2a99c72d4e727391850da2870b97863223f42dd0...e3608b160becaccdd7b069de9ff18ba5ecad5fa3#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">v2.2.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">v2.2.<span class="idiff left right">3</span></span></pre>
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<li id="1d03bbf095557f92ea6b6f914caa2d3bb64b1772">
<a href="https://salsa.debian.org/med-team/bcalm/-/compare/2a99c72d4e727391850da2870b97863223f42dd0...e3608b160becaccdd7b069de9ff18ba5ecad5fa3#1d03bbf095557f92ea6b6f914caa2d3bb64b1772"><strong>bidirected-graphs-in-bcalm2/bidirected-graphs-in-bcalm2.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ There are several ways of representing bi-directed graphs. Here we describe the</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Fig1</span><span class="p">](</span><span class="sx" style="color: #d14;">fig1.png</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown">Note that we draw the fromSign next to the "from" vertex, and the toSign next to the "to" vertex. In other words, the following <span class="idiff left right">graph is equivalent to the one above</span>:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">Note that we draw the fromSign next to the "from" vertex, and the toSign next to the "to" vertex. In other words, the following <span class="idiff left right">two graph are equivalent</span>:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Fig2</span><span class="p">](</span><span class="sx" style="color: #d14;">fig2.png</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/2a99c72d4e727391850da2870b97863223f42dd0...e3608b160becaccdd7b069de9ff18ba5ecad5fa3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcalm (2.2.3-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- David Parsons <david.parsons@inria.fr> Thu, 20 Aug 2020 15:53:06 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">bcalm (2.2.2-1.1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Non-maintainer upload.</span>
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<a href="https://salsa.debian.org/med-team/bcalm/-/compare/2a99c72d4e727391850da2870b97863223f42dd0...e3608b160becaccdd7b069de9ff18ba5ecad5fa3#a08e8d09cd4ef472df3d2d101176256178ed50b7"><strong>scripts/abundance_stats.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">os</span></span>
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<pre style="margin: 0;">+<span id="LC3" 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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"prints some abundance statitics of a unitigs FASTA file produced by BCALM"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"arguments: unitigs.fa"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># https://www.biostars.org/p/710/#1412</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">groupby</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fasta_iter</span><span class="p">(</span><span class="n" style="color: #333;">fasta_name</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;"> given a fasta file. yield tuples of header, sequence</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ditch the boolean (x[0]) and just keep the header or sequence since</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we know they alternate.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">faiter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">,</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">line</span><span class="p">:</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">">"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">header</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">faiter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># drop the ">"</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">header</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>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># join all sequence lines to one.</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">faiter</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">unitigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</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="LC25" class="line" lang="python"><span class="n" style="color: #333;">abundances</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">totsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">unitig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_iter</span><span class="p">(</span><span class="n" style="color: #333;">unitigs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">field</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"km:f:"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">field</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>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(abundance)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">abundance</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;">float</span><span class="p">(</span><span class="n" style="color: #333;">abundance</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># convert to rounded int</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">abundances</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">abundance</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;">totsize</span><span class="p">[</span><span class="n" style="color: #333;">abundance</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;">unitig</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counter</span><span class="p">(</span><span class="n" style="color: #333;">abundances</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;">"'value' : 'number of unitigs having this mean abundance value' : 'total size of unitigs having this mean abundance'"</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;">for</span> <span class="n" style="color: #333;">val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span><span class="s" style="color: #d14;">":"</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="n" style="color: #333;">val</span><span class="p">],</span><span class="s" style="color: #d14;">':'</span><span class="p">,</span><span class="n" style="color: #333;">totsize</span><span class="p">[</span><span class="n" style="color: #333;">val</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span></pre>
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