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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-nanomath">Debian Med / python-nanomath</a>
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<h4>
Commits:
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-nanomath/-/commit/fe1a2b9e7515451515b892d905ac6c361a52ff32">fe1a2b9e</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-08-21T21:59:14+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.0</pre>
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<strong><a href="https://salsa.debian.org/med-team/python-nanomath/-/commit/a6312d8761c00a17a19e5bf4e550d0db413de77a">a6312d87</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-09-01T19:27:53+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.1+ds</pre>
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<h4>8 changed files:</h4>
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<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<a href="#c721ed908bd00486c8fdcff084a92306d03e39eb">
nanomath.egg-info/PKG-INFO
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<a href="#f6cc5439d9297a99adcd89f264e3e63f2f21c678">
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nanomath.egg-info/SOURCES.txt
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<a href="#9428f5194cf3ac485510e911d6e0e1ee883c5e0e">
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nanomath.egg-info/requires.txt
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<a href="#bd8fd9949a7d37dd1ed7e503c3f6e15c777068ab">
nanomath/nanomath.py
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<a href="#d53a95c2a92a11bea71b033634233d5fa3e77146">
nanomath/version.py
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/python-nanomath/-/compare/da27f0263a64e9de105a1696cdb1f8544fbe6214...a6312d8761c00a17a19e5bf4e550d0db413de77a#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.2</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: nanomath</span>
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: <span class="idiff left right">0.23.2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: <span class="idiff left right">1.0.1</span></span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A few simple math function for other Oxford Nanopore processing scripts</span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/wdecoster/nanomath</span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Wouter De Coster</span>
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<td class="diff-line-num old_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">Author-email: decosterwouter@gmail.com</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">MIT</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">GPLv3</span></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="plaintext">Description: # nanomath</span>
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<td class="diff-line-num old_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> </span>
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<li id="561b88e19de321ca62c7590bbb350765fb110905">
<a href="https://salsa.debian.org/med-team/python-nanomath/-/compare/da27f0263a64e9de105a1696cdb1f8544fbe6214...a6312d8761c00a17a19e5bf4e550d0db413de77a#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" 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="24" 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">@@ -24,14 +24,14 @@ INSTALLATION</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">.. code:: bash</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> <span class="idiff left right"> </span>pip install nanomath</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> pip install nanomath</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">| or</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">| |install with conda|</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">::</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> <span class="idiff left right"> </span>conda install -c bioconda nanomath</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> conda install -c bioconda nanomath</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">STATUS</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">------</span>
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<a href="https://salsa.debian.org/med-team/python-nanomath/-/compare/da27f0263a64e9de105a1696cdb1f8544fbe6214...a6312d8761c00a17a19e5bf4e550d0db413de77a#c721ed908bd00486c8fdcff084a92306d03e39eb"><strong>nanomath.egg-info/PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.2</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: nanomath</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: <span class="idiff left right">0.23.2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: <span class="idiff left right">1.0.1</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A few simple math function for other Oxford Nanopore processing scripts</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/wdecoster/nanomath</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Wouter De Coster</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: decosterwouter@gmail.com</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">MIT</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">GPLv3</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Description: # nanomath</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> </span>
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<a href="https://salsa.debian.org/med-team/python-nanomath/-/compare/da27f0263a64e9de105a1696cdb1f8544fbe6214...a6312d8761c00a17a19e5bf4e550d0db413de77a#f6cc5439d9297a99adcd89f264e3e63f2f21c678"><strong>nanomath.egg-info/SOURCES.txt</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">LICENSE</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">MANIFEST.in</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">README.rst</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">setup.cfg</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">setup.py</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">nanomath/__init__.py</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">nanomath/nanomath.py</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">nanomath/test_nanomath.py</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">nanomath/version.py</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">nanomath.egg-info/PKG-INFO</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">nanomath.egg-info/SOURCES.txt</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">nanomath.egg-info/dependency_links.txt</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">nanomath.egg-info/requires.txt</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">nanomath.egg-info/top_level.txt</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pandas</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">numpy>1.8</span></pre>
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<a href="https://salsa.debian.org/med-team/python-nanomath/-/compare/da27f0263a64e9de105a1696cdb1f8544fbe6214...a6312d8761c00a17a19e5bf4e550d0db413de77a#bd8fd9949a7d37dd1ed7e503c3f6e15c777068ab"><strong>nanomath/nanomath.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,14 +20,16 @@ calc_read_stats(dataframe)</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</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;">math</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">log</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</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;">deprecated</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deprecated</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">math</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">log</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Stats</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">df</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">number_of_reads</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;">df</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">number_of_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_with_readIDs</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"readIDs"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"aligned_lengths"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">number_of_bases_aligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"aligned_lengths"</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">median_read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</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">@@ -39,16 +41,71 @@ class Stats(object):</td>
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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="s" style="color: #d14;">"channelIDs"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">active_channels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">unique</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"channelIDs"</span><span class="p">]).</span><span class="n" style="color: #333;">size</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"quals"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualgroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">15</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># needs 5 elements in current implementation</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>qualgroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">15</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># needs 5 elements in current implementation</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mean_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">median_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">top5_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quals"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">top5_quals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"quals"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reads_above_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">reads_above_qual</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">qualgroups</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_top5_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quals"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_top5_quals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">col</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"quals"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reads_above_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">reads_above_qual</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_qualgroups</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">long_features_as_string</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"""formatting long features to a string to print for legacy stats output"""</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">top5_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">long_feature_as_string_top5</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_top5_lengths</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">top5_quals</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">long_feature_as_string_top5</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_top5_quals</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reads_above_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">long_feature_as_string_above_qual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reads_above_qual</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">long_feature_as_string_top5</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">field</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"""for legacy stats output"""</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_with_readIDs</span><span class="p">:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ("</span> <span class="o" style="font-weight: 600;">+</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"; "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">field</span><span class="p">]</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ("</span> <span class="o" style="font-weight: 600;">+</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">field</span><span class="p">]</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">long_feature_as_string_above_qual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">field</span><span class="p">):</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">"""for legacy stats output"""</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">format_above_qual_line</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">field</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>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format_above_qual_line</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">entry</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="s" style="color: #d14;">"""for legacy stats output"""</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">numberAboveQ</span><span class="p">,</span> <span class="n" style="color: #333;">megAboveQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entry</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{} ({}%) {}Mb"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">numberAboveQ</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">numberAboveQ</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">number_of_reads</span><span class="p">),</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">ndigits</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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">megAboveQ</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</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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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"""for tsv stats output"""</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">statdict</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">statdict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">key</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">statdict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{:.1f}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">unwind_long_features_top5</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'_top5_lengths'</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'longest_read_(with_Q)'</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">unwind_long_features_top5</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'_top5_quals'</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'highest_Q_read_(with_length)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">unwind_long_features_above_qual</span><span class="p">(</span><span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'_reads_above_qual'</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Reads'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">v</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">statdict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">k</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">)}</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unwind_long_features_top5</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="s" style="color: #d14;">"""for tsv stats output"""</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span><span class="p">,</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)):</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">label</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 class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">ndigits</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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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">ndigits</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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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unwind_long_features_above_qual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">"""for tsv stats output"""</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span><span class="p">,</span> <span class="n" style="color: #333;">label</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">],</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'>Q{}:'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_qualgroups</span><span class="p">]):</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">numberAboveQ</span><span class="p">,</span> <span class="n" style="color: #333;">megAboveQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entry</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">numberAboveQ</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">number_of_reads</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">label</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{} ({}%) {}Mb"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">numberAboveQ</span><span class="p">,</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">percentage</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</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="LC108" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">megAboveQ</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</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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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_N50</span><span class="p">(</span><span class="n" style="color: #333;">readlengths</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">@@ -59,20 +116,19 @@ def get_N50(readlengths):</td>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">readlengths</span><span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">where</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">cumsum</span><span class="p">(</span><span class="n" style="color: #333;">readlengths</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">readlengths</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">deprecated</span></span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_length_outliers</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">columnname</span><span class="p">):</span></span>
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63
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">"""Remove records with length-outliers above 3 standard deviations from the median."""</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="n" style="color: #333;">columnname</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="n" style="color: #333;">columnname</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">std</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="n" style="color: #333;">columnname</span><span class="p">]))]</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">phred_to_percent</span><span class="p">(</span><span class="n" style="color: #333;">phred</span><span class="p">):</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">**</span> <span class="p">(</span><span class="n" style="color: #333;">phred</span> <span class="o" style="font-weight: 600;">/</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">deprecated</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">errs_tab</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">"""Generate list of error rates for qualities less than equal than n."""</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">**</span><span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">/</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n</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="LC129" class="line" lang="python"></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">deprecated</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">qround</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">tab</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">errs_tab</span><span class="p">(</span><span class="mi" style="color: #099;">128</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate average basecall quality of a read.</span></span>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,44 +147,22 @@ def ave_qual(quals, qround=False, tab=errs_tab(128)):</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">median_qual</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="s" style="color: #d14;">"""Receive the integer quality scores of a read and return the median quality for that read."""</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_top_5</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"readIDs"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"readIDs"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">re<span class="idiff left">s</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">ascending</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span> \</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">re<span class="idiff left right">turn</span></span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">ascending</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span> \</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">)[</span><span class="n" style="color: #333;">values</span><span class="p">]</span> \</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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="LC156" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">itertuples</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"readIDs"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ("</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"; "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ("</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reads_above_qual</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">numberAboveQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qual</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">megAboveQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1e6</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{} ({}%) {}Mb"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">numberAboveQ</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">numberAboveQ</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;">df</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)),</span> <span class="n" style="color: #333;">ndigits</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="LC119" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">megAboveQ</span><span class="p">,</span> <span class="n" style="color: #333;">ndigits</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="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">feature_list</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">padding</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">15</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="s" style="color: #d14;">'{:>{},.1f}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">],</span> <span class="n" style="color: #333;">padding</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;">stats</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC125" 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="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">])</span> <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;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">index</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NA"</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <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;">stats</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numberAboveQ</span><span class="p">,</span> <span class="n" style="color: #333;">megAboveQ</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_stats</span><span class="p">(</span><span class="n" style="color: #333;">datadfs</span><span class="p">,</span> <span class="n" style="color: #333;">outputfile</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]):</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_stats</span><span class="p">(</span><span class="n" style="color: #333;">datadfs</span><span class="p">,</span> <span class="n" style="color: #333;">outputfile</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">as_tsv</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">"""Call calculation functions and write stats file.</span></span>
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133
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"></span>
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134
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> This function takes a list of DataFrames,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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">@@ -140,6 +174,26 @@ def write_stats(datadfs, outputfile, names=[]):</td>
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140
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">output</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;">outputfile</span><span class="p">,</span> <span class="s" style="color: #d14;">'wt'</span><span class="p">)</span></span>
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141
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>
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142
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Stats</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">datadfs</span><span class="p">]</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">as_tsv</span><span class="p">:</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">df</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;">DataFrame</span><span class="p">([</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">to_dict</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;">stats</span><span class="p">]).</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Metrics'</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">names</span><span class="p">:</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">names</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'dataset'</span><span class="p">]</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</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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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">write_stats_legacy</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">datadfs</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_stats_legacy</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">datadfs</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="s" style="color: #d14;"> Legacy method to write out stats.</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> Will add padding to pretty print the table, and contain section headers</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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143
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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144
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="s" style="color: #d14;">"Number of reads"</span><span class="p">:</span> <span class="s" style="color: #d14;">"number_of_reads"</span><span class="p">,</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">"Total bases"</span><span class="p">:</span> <span class="s" style="color: #d14;">"number_of_bases"</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">@@ -170,16 +224,29 @@ def write_stats(datadfs, outputfile, names=[]):</td>
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170
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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171
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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;">pass</span></span>
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172
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226
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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="nb" style="color: #0086b3;">all</span><span class="p">([</span><span class="s" style="color: #d14;">"quals"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">df</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">df</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">datadfs</span><span class="p">]):</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <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;">stats</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">long_features_as_string</span><span class="p">()</span></span>
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173
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">long_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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174
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="s" style="color: #d14;">"Top 5 longest reads and their mean basecall quality score"</span><span class="p">:</span></span>
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175
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"top5_lengths"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)],</span></span>
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176
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="s" style="color: #d14;">"Top 5 highest mean basecall quality scores and their read lengths"</span><span class="p">:</span></span>
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177
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"top5_quals"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)],</span></span>
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178
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="s" style="color: #d14;">"Number, percentage and megabases of reads above quality cutoffs"</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"reads_above_qual"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">">Q"</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;">q</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">qualgroups</span><span class="p">]],</span></span>
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<td class="diff-line-num new new_line" data-linenumber="235" 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">
235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"reads_above_qual"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">">Q"</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;">q</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>qualgroups</span><span class="p">]],</span></span>
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180
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lf</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">long_features</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()):</span></span>
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">lf</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i<span class="idiff left right">ndex</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">write</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">long_features</span><span class="p">[</span><span class="n" style="color: #333;">lf</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">feature_list</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">long_features</span><span class="p">[</span><span class="n" style="color: #333;">lf</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="p">)))</span></span></pre>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">long_features</span><span class="p">[</span><span class="n" style="color: #333;">lf</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">],</span> <span class="n" style="color: #333;">feature_list</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stats</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">feature</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">long_features</span><span class="p">[</span><span class="n" style="color: #333;">lf</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="LC243" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">index</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">feature_list</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">padding</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">15</span><span class="p">):</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="s" style="color: #d14;">'{:>{},.1f}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">],</span> <span class="n" style="color: #333;">padding</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;">stats</span><span class="p">])</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">])</span> <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;">s</span><span class="p">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">feature</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">index</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NA"</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <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;">stats</span><span class="p">])</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-nanomath/-/compare/da27f0263a64e9de105a1696cdb1f8544fbe6214...a6312d8761c00a17a19e5bf4e550d0db413de77a#d53a95c2a92a11bea71b033634233d5fa3e77146"><strong>nanomath/version.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" 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;">"<span class="idiff left right">0.23.2</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" 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;">"<span class="idiff left right">1.0.1</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-nanomath/-/compare/da27f0263a64e9de105a1696cdb1f8544fbe6214...a6312d8761c00a17a19e5bf4e550d0db413de77a#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">@@ -15,7 +15,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC15" 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;">'https://github.com/wdecoster/nanomath'</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;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Wouter De Coster'</span><span class="p">,</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" 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;">'decosterwouter@gmail.com'</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;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right">MIT</span>'</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;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right">GPLv3</span>'</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;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'Development Status :: 4 - Beta'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'Intended Audience :: Science/Research'</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">@@ -29,6 +29,6 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nanopore sequencing plotting quality control'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</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;">python_requires</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'pandas'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numpy>1.8'</span><span class="p">,</span> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'pandas'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numpy>1.8'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'Python-Deprecated'</span></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;">package_dir</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'nanomath'</span><span class="p">:</span> <span class="s" style="color: #d14;">'nanomath'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">data_files</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"LICENSE"</span><span class="p">])])</span></span></pre>
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