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GitLab

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<h3>

Nilesh Patra pushed to branch master

at <a href="https://salsa.debian.org/med-team/xpore">Debian Med / xpore</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/xpore/-/commit/d07611b8ee23509e5e566a09a41672bb79ae5805">d07611b8</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-10-19T16:37:55+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/xpore/-/commit/5af9ac1c7c609425b02dee17ff516291af216ddd">5af9ac1c</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-10-19T16:37:55+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.1'

Update to upstream version '2.1'

with Debian dir 20cb41edd838158d49404c3c347a82a69fa511b5</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/xpore/-/commit/bea8751ee62ee65ba9720fbfce3f73d3ea59108c">bea8751e</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-10-19T16:38:52+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>18 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">

.gitignore

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

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<li class="file-stats">

<a href="#7f7c65c14002fc27910334d1ca5c1c44b24b3153">

<span class="new-file">

+

docs/source/citing.rst

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<a href="#f2098660f51003bbd0e63b1091ba2f00fc85678d">

docs/source/scripts.rst

→

docs/source/cmd.rst

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<li class="file-stats">

<a href="#aded7756cdea7c289134466a0d54da4f26d43abb">

docs/source/conf.py

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<li class="file-stats">

<a href="#0fc9a02d33ddce68dac5cde8db895c5676822876">

<span class="new-file">

+

docs/source/data.rst

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<li class="file-stats">

<a href="#068563c549edfdcd5fb618b782d9f1a8e7e6b8d5">

<span class="new-file">

+

docs/source/help.rst

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<li class="file-stats">

<a href="#62df078594b947ca6f787a59ae6ddefabce9fcad">

docs/source/index.rst

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<a href="#2d9c0c62cdf7d42edd7e9a56b0879a0286f40f1c">

docs/source/installation.rst

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<li class="file-stats">

<a href="#738b9327c5f964a5073534a9ccb9a532ad1bd996">

docs/source/quickstart.rst

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<a href="#6cae7b858fce19b90be27a9dd23562819df3b9ad">

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−

gtf

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

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<li class="file-stats">

<a href="#04761e70c55cc8f0968e64d33b23960603d7f179">

xpore/__init__.py

</a>

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<li class="file-stats">

<a href="#748b28739f28a31150cbb229c1ccfffa96230202">

xpore/scripts/dataprep.py

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<li class="file-stats">

<a href="#914848e996270683a7a728dd93078d41e21774e1">

xpore/scripts/diffmod.py

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<li class="file-stats">

<a href="#845edb6ada5749d19a27b846df666a2bb131a9a9">

<span class="new-file">

+

xpore/scripts/postprocessing.py

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<li class="file-stats">

<a href="#f3c38bd4ea15b9ca3d6bc37bad514c99766dd6b6">

<span class="new-file">

+

xpore/scripts/xpore.py

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</ul>

<h4>Changes:</h4>

<li id="a5cc2925ca8258af241be7e5b0381edf30266302">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="131" 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="131" 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">@@ -131,3 +131,6 @@ dmypy.json</td>

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131

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131

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="132" 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">

132

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<td class="new_line diff-line-num" data-linenumber="132" 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">

132

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"># Pyre type checker</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="133" 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">

133

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133

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext">.pyre/</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="134" 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">

134

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="135" 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="LC135" class="line" lang="plaintext"># DS store</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.DS_Store</span></pre>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="20" 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">@@ -20,17 +20,20 @@ To install the latest release with PyPI (recommended), run</td>

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<td class="new_line diff-line-num" data-linenumber="20" 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="LC20" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="21" 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="LC21" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">```</span><span class="s" style="color: #d14;">sh</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="s" style="color: #d14;">$ pip install xpore</span> </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="s" style="color: #d14;">$ pyensembl install --release 91 --species homo_sapiens</span>  <span class="c1" style="color: #998; font-style: italic;"># please specify the compatible Ensembl release with your data when you install it.</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">```</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="24" 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="LC24" class="line" lang="markdown"><span class="nn" style="color: #555;">---</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="new_line diff-line-num" data-linenumber="26" 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="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Documentation</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="27" 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="LC27" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="28" 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="LC27" class="line" lang="markdown"><span class="s" style="color: #d14;">Please refer to the xPore documention ([https://xpore.readthedocs.io](https://xpore.readthedocs.io)) for additional information, a quick start guide, and details on the data processing and output file format.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" 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="LC28" class="line" lang="markdown">Please refer to our xPore documentation (<span class="p">[</span><span class="nv" style="color: #008080;">https://xpore.readthedocs.io</span><span class="p">](</span><span class="sx" style="color: #d14;">https://xpore.readthedocs.io</span><span class="p">)</span>) for additional information, a quick start guide, and details on the data processing and output file format.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="30" 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="LC30" class="line" lang="markdown">xPore is described in details in <span class="p">[</span><span class="nv" style="color: #008080;">Pratanwanich et al. *Nat Biotechnol* (2021)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1038/s41587-021-00949-w</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC29" class="line" lang="markdown"><span class="s" style="color: #d14;"><span class="idiff left right">xPore is described in detail in a preprint (https://www.biorxiv.org/content/10.1101/2020.06.18.160010v1)</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="32" 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="LC32" class="line" lang="markdown"><span class="p"><span class="idiff left right">---</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" 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="LC33" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="34" 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="LC34" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Release History</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="35" 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="LC35" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="36" 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="LC33" class="line" lang="markdown"><span class="s" style="color: #d14;">The current release is xPore v<span class="idiff left right">1.0.</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="36" 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="LC36" class="line" lang="markdown">The current release is xPore v<span class="idiff left right">2.1. </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="37" 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="LC37" class="line" lang="markdown"></span>

</pre>

</td>

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

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<td class="new_line diff-line-num" data-linenumber="38" 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="LC38" class="line" lang="markdown">Please refer to the github release history for previous releases: https://github.com/GoekeLab/xpore/releases</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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="41" 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">@@ -38,17 +41,19 @@ Please refer to the github release history for previous releases: https://github</td>

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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="42" 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="LC42" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Citing xPore</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown">If you use xPore in your research, please cite</span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="44" 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="LC43" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Ploy N. Pratanwanich, Ploy N. et al. "Detection of differential RNA modifications from direct RNA sequencing of human cell lines". *bioRxiv* (2020) doi: https://doi.org/10.1101/2020.06.18.160010</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.biorxiv.org/content/10.1101/2020.06.18.160010v1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown">If you use xPore in your research, please cite </span>

</pre>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" 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="LC46" class="line" lang="markdown">Ploy N. Pratanwanich, et al. Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. <span class="ge" style="font-style: italic;">*Nat Biotechnol*</span> (2021), <span class="p">[</span><span class="nv" style="color: #008080;">https://doi.org/10.1038/s41587-021-00949-w</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1038/s41587-021-00949-w</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="p">---</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="47" 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="LC49" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <span class="idiff left right">Contact</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <span class="idiff left right">Getting Help</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown">xPore is maintained by <span class="p">[</span><span class="nv" style="color: #008080;">Ploy N. Pratanwanich</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ploy-np</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">Jonathan Goeke</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/jonathangoeke</span><span class="p">)</span> from the Genome Institute of Singapore, A<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>STAR. </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="52" 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">

</td>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown">If you want to contribute, please leave an issue. </span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">We appreciate your feedback and questions! You can report any error or suggestion related to xPore as an <span class="p">[</span><span class="nv" style="color: #008080;">issue on github</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/GoekeLab/xpore/issues</span><span class="p">)</span>. If you have questions related to the manuscript, data, or any general comment or suggestion please use the <span class="p">[</span><span class="nv" style="color: #008080;">Discussions</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/GoekeLab/xpore/discussions</span><span class="p">)</span>.</span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">Thank you!</span>

</pre>

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

</pre>

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<td class="new_line diff-line-num new" data-linenumber="56" 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="LC56" class="line" lang="markdown"><span class="p">---</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" 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="LC58" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Contact</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="59" 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="LC59" class="line" lang="markdown">xPore is maintained by <span class="p">[</span><span class="nv" style="color: #008080;">Ploy N. Pratanwanich</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ploy-np</span><span class="p">)</span>, <span class="p">[</span><span class="nv" style="color: #008080;">Yuk Kei Wan</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/yuukiiwa</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">Jonathan Goeke</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/jonathangoeke</span><span class="p">)</span> from the Genome Institute of Singapore, A<span class="se" style="color: #d14;">\*</span>STAR. </span></pre>

</td>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">xpore (2.1-1) unstable; urgency=medium</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" 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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2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team Upload.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" 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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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version 2.1</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" 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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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Standards version: 4.6.0</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" 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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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org>  Tue, 19 Oct 2021 16:38:22 +0530</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1" 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">

1

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<td class="new_line diff-line-num" 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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">xpore (1.0-2) unstable; urgency=medium</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="new_line diff-line-num" 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">

10

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

</pre>

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

3

</td>

<td class="new_line diff-line-num" data-linenumber="11" 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">

11

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  * Team Upload.</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="7f7c65c14002fc27910334d1ca5c1c44b24b3153">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#7f7c65c14002fc27910334d1ca5c1c44b24b3153"><strong>docs/source/citing.rst</strong></a>

<hr>

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<td class="new_line diff-line-num new" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. _citing:</span>

</pre>

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

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

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Citing xPore</span>

</pre>

</td>

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

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

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">==================</span>

</pre>

</td>

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

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<td class="new_line diff-line-num new" data-linenumber="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">If you use xPore in your research, please cite</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Ploy N. Pratanwanich, et al., Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. *Nat Biotechnol* (2021), `https://doi.org/10.1038/s41587-021-00949-w <https://doi.org/10.1038/s41587-021-00949-w>`_.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Thank you!</span></pre>

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<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#f2098660f51003bbd0e63b1091ba2f00fc85678d"><strong>docs/source/scripts.rst</strong>

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<strong>docs/source/cmd.rst</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.. _<span class="idiff left right">scripts</span>:</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. _<span class="idiff left right">cmd</span>:</span>

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

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<td class="new_line diff-line-num 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"><span class="idiff left right">Scrip</span>ts</span>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num 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="LC4" class="line" lang="plaintext">==========</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">Command line argumen</span>ts</span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="4" 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="LC4" class="line" lang="plaintext">==========<span class="idiff left right">=============</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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">We provide 2 main scripts to run the analysis of differential RNA modifications as the following.</span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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"></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,27 +10,20 @@ We provide 2 main scripts to run the analysis of differential RNA modifications</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

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<td class="new_line diff-line-num" data-linenumber="11" 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="LC11" class="line" lang="plaintext">* Input</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="13" 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="LC13" class="line" lang="plaintext">Output files from `nanopolish eventalgin`. Please refer to :ref:`Data preparation <preparation>` for the full Nanopolish command.</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="13" 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="LC14" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="13" 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="LC15" class="line" lang="plaintext">* Usage example</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Output files from ``nanopolish eventalgin``. Please refer to :ref:`Data preparation <preparation>` for the full Nanopolish command.</span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">=================================   ==========  ===================  ============================================================================================================</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Argument name<span class="idiff left right">(s)</span>                    Required    Default value         Description</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Argument name<span class="idiff left right">   </span>                    Required    Default value         Description</span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">=================================   ==========  ===================  ============================================================================================================</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">--eventalign=FILE                   Yes         NA                    Eventalign filepath, the output from nanopolish.         </span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">--summary=FILE                      Yes         NA                    Eventalign summary filepath, the output from nanopolish.</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">--out_dir=DIR                       Yes         NA                    Output directory.</span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">--ensembl=NUM                       No          91                    Ensembl version for gene-transcript mapping.</span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">--species=STR                       No          homo_sapiens          Species for ensembl gene-transcript mapping.</span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">--customised_genome                 No          False                 If customised genome provided.</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">--reference_name                    No          NA                    fasta reference name.</span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">--annotation_name                   No          NA                    gtf annotation name.</span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">--gtf_path_or_url                   No          NA                    gtf file path or url.</span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">--transcript_fasta_paths_or_urls    No          NA                    Transcript fasta paths or urls.</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">--gtf_path_or_url                   No          NA                    GTF file path or url used for mapping transcriptomic to genomic coordinates.</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">--transcript_fasta_paths_or_urls    No          NA                    Transcript FASTA paths or urls used for mapping transcriptomic to genomic coordinates.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">--skip_eventalign_indexing          No          False                 To skip indexing the eventalign nanopolish output.</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">--genome                            No          False                 To run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates.</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">--n_processes=NUM                   No          1                     Number of processes to run.</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">--readcount_max=NUM                 No          1000                  Maximum read counts per gene.</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">--readcount_min=NUM                 No          1                     Minimum read counts per gene.</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">--resume                            No          False                 With this argument, the program will resume from the previous run.</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"></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">@@ -51,14 +44,12 @@ data.readcount          csv             Summary of readcounts per gene.</td>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">* Input</span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">Output files from `xpore-dataprep`.</span>

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<td class="new_line diff-line-num old" data-linenumber="47" 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="LC55" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">* Usage example</span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Output files from ``xpore-dataprep``.</span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">===================  ==========  ===============      ==============================================================================</span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">Argument name<span class="idiff left right">(s)</span>      Required    Default value       Description</span>

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<td class="new_line diff-line-num new" data-linenumber="50" 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="LC50" class="line" lang="plaintext">Argument name<span class="idiff left right">   </span>      Required    Default value       Description</span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">===================  ==========  ===============      ==============================================================================</span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">--config=FILE           Yes         NA                Y<span class="idiff left right">aml</span> configuraion filepath.</span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">--config=FILE           Yes         NA                Y<span class="idiff left">AML</span> configur<span class="idiff right">t</span>aion filepath.</span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">--n_processes=NUM       No          1                 Number of processes to run.</span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">--save_models           No          False             With this argument, the program will save the model parameters for each id.</span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">--resume                No          False             With this argument, the program will resume from the previous run.</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">@@ -73,4 +64,17 @@ File name                File type           Description</td>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">diffmod.table            csv                 Output table information of differential modification rates. Please refer to :ref:`Output table description <outputtable>` for the full description.   </span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">diffmod.log              txt                 Gene/Transcript ids being processed.</span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">======================  ===============     =================================================================================================================================================</span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">   </span></pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">``xpore-postprocessing``</span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">**************************</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">* Input</span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">The ``diffmod.table`` file  from ``xpore-diffmod``.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">======================  ===============     =======================================================================</span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">Argument name            Required           Description</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">======================  ===============     =======================================================================</span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">--diffmod_dir            Yes                Path of the directory containing ``diffmod.table``.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">======================  ===============     =======================================================================</span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="aded7756cdea7c289134466a0d54da4f26d43abb">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#aded7756cdea7c289134466a0d54da4f26d43abb"><strong>docs/source/conf.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">@@ -26,9 +26,9 @@ copyright = '2020, Ploy N. Pratanwanich'</td>

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<pre style="margin: 0;"> <span id="LC26" 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;">'Ploy N. Pratanwanich'</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The short X.Y version</span></span>

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<pre style="margin: 0;">-<span id="LC29" 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</span>.0'</span></span>

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<pre style="margin: 0;">+<span id="LC29" 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">2</span>.0'</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">1</span>.0'</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">2</span>.0'</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- General configuration ---------------------------------------------------</span></span>

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<li id="0fc9a02d33ddce68dac5cde8db895c5676822876">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#0fc9a02d33ddce68dac5cde8db895c5676822876"><strong>docs/source/data.rst</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. _data:</span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Data</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">======</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">You can find the links to all preprocessed data used in our manuscript at Zenodo `for the SGNEx data <https://doi.org/10.5281/zenodo.4604945>`_ and `for the others samples <https://doi.org/10.5281/zenodo.4587661>`_.</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">All the raw fast5 and fastq files are also available at `ENA <https://www.ebi.ac.uk/ena/browser/view/PRJEB40872>`_ and `SGNEx <https://github.com/GoekeLab/sg-nex-data>`_. Please refer to our Supplementary Table S7 in our manuscript for full details of data download.</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Note that all HEK293T-KO samples can be used as unmodified (m6A) controls for any other data set generated with the same RNA kit (SQK-RNA001).</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">If the cells are genetically different, we recommend to perform variant calling before finalising the list of differentially modified sites in order to remove false positives.</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span></pre>

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<li id="068563c549edfdcd5fb618b782d9f1a8e7e6b8d5">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#068563c549edfdcd5fb618b782d9f1a8e7e6b8d5"><strong>docs/source/help.rst</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. _help:</span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Getting Help</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">==================</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">We appreciate your feedback and questions! You can report any error or suggestion related to xPore as an `issue on github <https://github.com/GoekeLab/xpore/issues>`_. If you have questions related to the manuscript, data, or any general comment or suggestion please use the `Discussions <https://github.com/GoekeLab/xpore/discussions>`_.</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Thank you!</span></pre>

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</li>

<li id="62df078594b947ca6f787a59ae6ddefabce9fcad">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#62df078594b947ca6f787a59ae6ddefabce9fcad"><strong>docs/source/index.rst</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">@@ -5,15 +5,18 @@</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Welcome to xPore's documentation!</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">=================================</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">xPore is a Python package for de<span class="idiff left right">tec</span>tion of differentail RNA modifications from Nanopore sequencing data.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">xPore is a Python package for <span class="idiff left">i</span>de<span class="idiff right">ntifica</span>tion of differentail RNA modifications from Nanopore sequencing data.</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

9

</td>

<td class="new_line diff-line-num" 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">

9

</td>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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">

10

</td>

<td class="new_line diff-line-num" 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">

10

</td>

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">To install the latest release, run::</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="11" 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">

11

</td>

<td class="new_line diff-line-num" data-linenumber="11" 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">

11

</td>

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="12" 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">

12

</td>

<td class="new_line diff-line-num" data-linenumber="12" 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">

12

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

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">    pip install xpore</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="13" 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">

13

</td>

<td class="new_line diff-line-num old" data-linenumber="13" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">    pyensembl install --release 91 --species homo_sapiens  # Please specify the compatible Ensembl release with your data when you install it.</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="14" 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">

14

</td>

<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="15" 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">

15

</td>

<td class="new_line diff-line-num" data-linenumber="14" 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">

14

</td>

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">See our :ref:`Installation page <installation>` for details.</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="16" 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">

16

</td>

<td class="new_line diff-line-num" data-linenumber="15" 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">

15

</td>

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="17" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" 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">

16

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">To check the version of xPore, run::</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="17" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" 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">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="17" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" 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">

18

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">    xpore -v</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="17" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" 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">

19

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="17" 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">

17

</td>

<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">To detect differential modifications, you can follow the instructions in our :ref:`Quickstart page <quickstart>`. </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="18" 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">

18

</td>

<td class="new_line diff-line-num" data-linenumber="21" 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">

21

</td>

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

<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="19" 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">

19

</td>

<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Contents</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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="29" 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">@@ -26,11 +29,18 @@ Contents</td>

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

<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">   outputtable</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="27" 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">

27

</td>

<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">   configuration</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="28" 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">

28

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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">   preparation</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="29" 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">

29

</td>

<td class="new_line diff-line-num old" data-linenumber="32" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">   scripts</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="30" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">   data</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="30" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="33" 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">

33

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">   cmd</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="30" 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="LC34" class="line" lang="plaintext">   citing</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">   help</span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Contacts</span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">--------</span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">xPore is maintained by `Ploy N. Pratanwanich <https://github.com/ploy-rukawa>`_ and `Jonathan Goeke <https://github.com/jonathangoeke>`_ from the Genome Institute of Singapore, A*STAR. </span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">If you use xPore in your research, please cite</span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Ploy N. Pratanwanich, et al.,Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. *Nat Biotechnol* (2021), `https://doi.org/10.1038/s41587-021-00949-w <https://doi.org/10.1038/s41587-021-00949-w>`_ </span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">xPore is maintained by `Ploy N. Pratanwanich <https://github.com/ploy-np>`_, `Yuk Kei Wan <https://github.com/yuukiiwa>`_ and `Jonathan Goeke <https://github.com/jonathangoeke>`_ from the Genome Institute of Singapore, A*STAR. </span>

</pre>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">If you want to contribute, please leave an issue in `our repo <https://github.com/GoekeLab/xpore>`_</span>

</pre>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>

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<br>

</li>

<li id="2d9c0c62cdf7d42edd7e9a56b0879a0286f40f1c">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#2d9c0c62cdf7d42edd7e9a56b0879a0286f40f1c"><strong>docs/source/installation.rst</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">@@ -10,7 +10,6 @@ PyPI installation (recommended)</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">::</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">    pip install xpore</span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">    pyensembl install --release 91 --species homo_sapiens  # please specify the compatible Ensembl release with your data when you install it.</span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Installation from our GitHub repository</span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">---------------------------------------</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">@@ -19,4 +18,4 @@ Installation from our GitHub repository</td>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">    git clone https://github.com/GoekeLab/xpore.git</span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">    cd xpore</span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">    python setup.py install</span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"><span class="idiff left right">    pyensembl install --release 91 --species homo_sapiens  # please specify the compatible Ensembl release with your data when you install it.</span></span></pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="738b9327c5f964a5073534a9ccb9a532ad1bd996">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#738b9327c5f964a5073534a9ccb9a532ad1bd996"><strong>docs/source/quickstart.rst</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Quickstart - Detection of differential RNA modifications</span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">=========================================================</span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Download and extract the demo dataset from our `<span class="idiff left">S3 bucket</span> <http://<span class="idiff right">s3.ap-southeast-1.amazonaws.com/all-public-data.store.genome.sg/xpore</span>/demo.tar.gz>`_::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Download and extract the demo dataset from our `<span class="idiff left">zenodo</span> <http<span class="idiff">s</span>://<span class="idiff right">zenodo.org/record/5162402/files</span>/demo.tar.gz>`_::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">    wget http://<span class="idiff left right">s3.ap-southeast-1.amazonaws.com/all-public-data.store.genome.sg/xpore</span>/demo.tar.gz</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" 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">    wget http<span class="idiff left">s</span>://<span class="idiff right">zenodo.org/record/5162402/files</span>/demo.tar.gz</span>

</pre>

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<td class="new_line diff-line-num" 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">    tar -xvf demo.tar.gz</span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">After extraction, you will find::</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="15" 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">@@ -15,20 +15,25 @@ After extraction, you will find::</td>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">    |-- data</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">        |-- HEK293T-METTL3-KO-rep1  # dataset dir</span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">        |-- HEK293T-WT-rep1 # dataset dir</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">    |-- demo.gtf # GTF (general transfer format) file for transcript-to-gene mapping  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">    |-- demo.fa # transcriptome reference FASTA file for transcript-to-gene mapping</span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Each dataset under the ``data`` directory contains the following directories:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">* ``fast5`` : Raw signal FAST5 files</span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">* ``fastq`` : Basecalled reads</span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">* ``bamtx`` : Transcriptome-aligned sequence</span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">* ``fast5`` : Raw signal<span class="idiff left right">,</span> FAST5 files</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">* ``fastq`` : Basecalled reads<span class="idiff left right">, FASTQ file</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">* ``bamtx`` : Transcriptome-aligned sequence<span class="idiff left right">, BAM file</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">* ``nanopolish``: Eventalign files obtained from `nanopolish eventalign <https://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html>`_</span>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">1. Preprocess the data for each data set using ``xpore-dataprep``. (This step will take approximately 5h for 1 million reads)::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Note that the FAST5, FASTQ and BAM files are required to obtain the eventalign file with Nanopolish, xPore only requires the eventalign file. See our :ref:`Data preparation page <preparation>` for details to obtain the eventalign file from raw reads.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="27" 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="LC30" class="line" lang="plaintext">1. Preprocess the data for each data set using ``xpore dataprep``. Note that the ``--gtf_or_gff`` and ``--transcript_fasta`` arguments are required to map transcriptomic to genomic coordinates when the ``--genome`` option is chosen, so that xPore can run based on genome coordinates. However, GTF is the recommended option. If GFF is the only file available, please note that the GFF file works with GENCODE or ENSEMBL FASTA files, but not UCSC FASTA files. We plan to remove the requirement of FASTA files in a future release.(This step will take approximately 5h for 1 million reads)::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">    # Within each dataset directory i.e. demo/data/HEK293T-METTL3-KO-rep1 and demo/data/HEK293T-WT-rep1, run</span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">    xpore<span class="idiff left right">-</span>dataprep \</span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">    xpore<span class="idiff left right"> </span>dataprep \</span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">    --eventalign nanopolish/eventalign.txt \</span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">    --summary nanopolish/summary.txt \</span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">    --gtf_or_gff ../../demo.gtf \</span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">    --transcript_fasta ../../demo.fa \</span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">    --out_dir dataprep \</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">    --genome  </span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" 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="45" 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">@@ -40,7 +45,7 @@ The output files are stored under ``dataprep`` in each  dataset directory:</td>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">* ``data.readcount`` : Summary of readcounts per gene</span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">* ``data.log`` : Log file</span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">Run ``xpore<span class="idiff left">-</span>dataprep -h`` to explore the full usage<span class="idiff right">.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Run ``xpore<span class="idiff left"> </span>dataprep -h`` <span class="idiff">or visit our :ref:`Command line arguments <cmd>` </span>to explore the full usage<span class="idiff right"> description. </span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">2. Prepare a ``.yml`` configuration file. With this YAML file, you can specify the information of your design experiment, the data directories, the output directory, and the method options.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">In the demo directory, there is an example configuration file ``Hek293T_config.yaml`` available that you can use as a starting template.</span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" 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">@@ -56,28 +61,22 @@ Below is how it looks like::</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">    out: ./out # output dir</span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="64" 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="LC59" class="line" lang="plaintext">    method:</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="64" 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="LC60" class="line" lang="plaintext">        prefiltering:</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="64" 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="LC61" class="line" lang="plaintext">            method: t-test</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="64" 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="LC62" class="line" lang="plaintext">            threshold: 0.1</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="64" 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="LC63" class="line" lang="plaintext">        stopping_criteria: 0.0001</span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">Note that if high accuracy is required, the ``prefiltering`` section should be removed and the processing time is accordingly longer.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">See the :ref:`Configuration file page <configuration>` for details.</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="65" 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="LC65" class="line" lang="plaintext">See the :ref:`Configuration file page <configuration>` for more details.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">3. Now that we have the data and the configuration file ready for modelling differential modifications using ``xpore-diffmod``. </span>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">    # At the demo directory where the configuration file is, run.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">    xpore<span class="idiff left right">-</span>diffmod --config Hek293T_config.yml</span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">    xpore<span class="idiff left right"> </span>diffmod --config Hek293T_config.yml</span>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="75" 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="LC74" class="line" lang="plaintext">The output files are generated within the ``out`` directory:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">* ``diffmod.table`` : Result table of differential RNA modification across all tested positions</span>

</pre>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">* ``diffmod.log`` : Log file</span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">Run ``xpore<span class="idiff left right">-</span>diffmod -h`` to explore the full usage.</span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">Run ``xpore<span class="idiff left"> </span>diffmod -h`` <span class="idiff">or visit our :ref:`Command line arguments <cmd>` </span>to explore the full usage<span class="idiff right"> description</span>.</span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">We can rank the significantly differentially modified sites based on ``pval_HEK293T-KO_vs_HEK293T-WT``. The results are shown below.::</span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"></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">@@ -88,9 +87,15 @@ We can rank the significantly differentially modified sites based on ``pval_HEK2</td>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">    ENSG00000159111   47824137  GGACA               -0.604056   7.614675e-24        -10.068479  ...      7.164075    4.257725       0.553929     0.353160           lower  2.294337e-10</span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">    ENSG00000114125  141745249  GGACT               -0.514980   2.779122e-19         -8.977134  ...      5.215243   20.598471       0.954968     0.347174           lower  1.304111e-06</span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"><span class="idiff left right">**Notes:**</span> We can consider only one modification type per k-mer by finding the majority ``mod_assignment`` of each k-mer. </span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"><span class="idiff left right">4. (Optional)</span> We can consider only one modification type per k-mer by finding the majority ``mod_assignment`` of each k-mer. </span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">For example, the majority of the modification means of ``GGACT`` (``mu_mod``) is lower than the non-modification counterpart (``mu_unmod``). </span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">This can be achieved by simply running ``groupby`` on the ``kmer`` and ``mod_assignment`` columns in Python.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">We can then remove those positions with the ``mod_assigment`` not in line with the majority in order to restrict ourselves with one modification type per kmer in the analysis.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">You can find more details in our paper.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">We can filter out those positions whose ``mod_assigment`` values are not in line with those of the majority in order to restrict ourselves with one modification type per kmer in the analysis.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">This can be done by running ``xpore postprocessing``.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">::</span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" 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="LC97" class="line" lang="plaintext">    xpore postprocessing --diffmod_dir out</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" 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="LC98" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="99" 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="LC99" class="line" lang="plaintext">With this command, we will get the final file in which only kmers with their ``mod_assignment`` different from the majority assigment of the corresponding kmer are removed. The output file ``majority_direction_kmer_diffmod.table`` is generated in the ``out`` directtory. You can find more details in our paper.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Run ``xpore postprocessing -h`` or visit our :ref:`Command line arguments <cmd>` to explore the full usage description.</span></pre>

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<br>

</li>

<li id="6cae7b858fce19b90be27a9dd23562819df3b9ad">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#6cae7b858fce19b90be27a9dd23562819df3b9ad"><strong>gtf</strong>

deleted

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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,7 +14,7 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__pkg_name__</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">    <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"MIT"</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="16" 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="LC16" class="line" lang="python">    <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'xpore is a python package for Nanopore data analysis of differential RNA modifications.'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'v<span class="idiff left right">1.0</span>'</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'v<span class="idiff left right">2.1</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;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">README</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="19" 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="LC19" class="line" lang="python">    <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text/markdown'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="20" 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="LC20" 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/GoekeLab/xpore'</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="30" 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">@@ -30,8 +30,7 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">            <span class="s" style="color: #d14;">'ujson>=4.0.1'</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">            <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;">python_requires</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">">=3.8"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="33" 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="LC33" class="line" lang="python">    <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"xpore-dataprep={}.scripts.dataprep:main"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">__pkg_name__</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="33" 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="LC34" class="line" lang="python">                                      <span class="s" style="color: #d14;">"xpore-diffmod={}.scripts.diffmod:main"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">__pkg_name__</span><span class="p">)]},</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="33" 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="LC33" class="line" lang="python">    <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"xpore={}.scripts.xpore:main"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">__pkg_name__</span><span class="p">)]},</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="35" 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="LC34" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Trove classifiers</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" 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="LC36" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># (https://pypi.python.org/pypi?%3Aaction=list_classifiers)</span></span>

</pre>

</td>

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<br>

</li>

<li id="04761e70c55cc8f0968e64d33b23960603d7f179">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#04761e70c55cc8f0968e64d33b23960603d7f179"><strong>xpore/__init__.py</strong></a>

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1

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<td class="new_line diff-line-num old" data-linenumber="1" 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="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;">"1.0"</span></span></pre>

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<td class="new_line diff-line-num" 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">\ No newline at end of file</td>

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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;">"2.0"</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="748b28739f28a31150cbb229c1ccfffa96230202">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#748b28739f28a31150cbb229c1ccfffa96230202"><strong>xpore/scripts/dataprep.py</strong></a>

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<td class="new_line diff-line-num old" data-linenumber="1" 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="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1" 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>

</pre>

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span><span class="n" style="color: #333;">re</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,8 +5,6 @@ import multiprocessing</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">h5py</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">csv</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ujson</span></span>

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<td class="new_line diff-line-num old" data-linenumber="8" 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="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyensembl</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">EnsemblRelease</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="8" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyensembl</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Genome</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">operator</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">itemgetter</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>

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<td class="new_line diff-line-num" 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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="12" 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">@@ -15,43 +12,6 @@ from io import StringIO</td>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">helper</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">misc</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_args</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentDefaultsHelpFormatter</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC20" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC21" class="line" lang="python">    <span class="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC22" class="line" lang="python">    <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'required arguments'</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC23" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Required arguments</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python">    <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--eventalign'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'eventalign'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'eventalign filepath, the output from nanopolish.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--summary'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'summary'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'eventalign summary filepath, the output from nanopolish.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--out_dir'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'out_dir'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'output directory.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC28" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC29" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Optional</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Use ensembl db</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC31" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--ensembl'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ensembl'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ensembl version for gene-transcript mapping.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">91</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC32" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--species'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'species'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'species for ensembl gene-transcript mapping.'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'homo_sapiens'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Use customised db</span></span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># These arguments will be passed to Genome from pyensembl</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC36" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--customised_genome'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'customised_genome'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'if customised genome provided.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC37" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--reference_name'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'reference_name'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'fasta reference name.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--annotation_name'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'annotation_name'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gtf annotation name.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--gtf_path_or_url'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gtf_path_or_url'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gtf file path or url.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--transcript_fasta_paths_or_urls'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'transcript_fasta_paths_or_urls'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'transcript fasta paths or urls.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC42" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--skip_eventalign_indexing'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'skip_eventalign_indexing'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'skip indexing the eventalign nanopolish output.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC44" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--features', dest='features', help='Signal features to extract.',type=list,default=['norm_mean'])</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC45" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--genome'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'genome'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'to run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC46" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'number of processes to run.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</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;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--chunk_size'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'chunk_size'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'number of lines from nanopolish eventalign.txt for processing.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000000</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;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--readcount_min'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'readcount_min'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'minimum read counts per gene.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC49" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--readcount_max'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'readcount_max'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'maximum read counts per gene.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</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;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--resume'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'resume'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'with this argument, the program will resume from the previous run.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#todo</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC51" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

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<td class="new_line diff-line-num old" data-linenumber="15" 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="LC54" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">index</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_result</span><span class="p">,</span><span class="n" style="color: #333;">pos_start</span><span class="p">,</span><span class="n" style="color: #333;">out_paths</span><span class="p">,</span><span class="n" style="color: #333;">locks</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="16" 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="LC16" class="line" lang="python">    <span class="n" style="color: #333;">eventalign_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">eventalign_result</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">([</span><span class="s" style="color: #d14;">'contig'</span><span class="p">,</span><span class="s" style="color: #d14;">'read_index'</span><span class="p">])</span></span>

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<td class="new_line diff-line-num" data-linenumber="17" 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="LC17" class="line" lang="python">    <span class="n" style="color: #333;">pos_end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pos_start</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" 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="26" 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">@@ -66,7 +26,7 @@ def index(eventalign_result,pos_start,out_paths,locks):</td>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">            <span class="n" style="color: #333;">pos_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos_end</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="29" 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="LC69" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parallel_index</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left">summary_filepath</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">chunk_size</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="29" 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="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parallel_index</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;">chunk_size</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="30" 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="LC30" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Create output paths and locks.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="71" 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="LC31" class="line" lang="python">    <span class="n" style="color: #333;">out_paths</span><span class="p">,</span><span class="n" style="color: #333;">locks</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(),</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="32" 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="LC32" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">out_filetype</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'index'</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" 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="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,25 +78,32 @@ def parallel_index(eventalign_filepath,summary_filepath,chunk_size,out_dir,n_pro</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Wait for all of the tasks to finish.</span></span>

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<td class="new_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">    <span class="n" style="color: #333;">task_queue</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">    </span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t2g</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">ensembl</span></span><span class="p">,</span><span class="n" style="color: #333;">g2t_mapping</span><span class="p">,</span><span class="n" style="color: #333;">df_eventalign_index</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="81" 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="LC81" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t2g</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left">fasta_dict</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">annotation_dict</span></span><span class="p">,</span><span class="n" style="color: #333;">g2t_mapping</span><span class="p">,</span><span class="n" style="color: #333;">df_eventalign_index</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">    <span class="n" style="color: #333;">tx_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">    <span class="n" style="color: #333;">t2g_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python">    <span class="n" style="color: #333;">transcripts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">ensembl</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gene_by_id</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gene_id</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">transcripts</span></span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tx</span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">id</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2t_mapping</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="125" 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="LC125" class="line" lang="python">    <span class="n" style="color: #333;">n_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df_eventalign_index</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p"><span class="idiff left">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">id</span></span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">transcripts</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">    <span class="n" style="color: #333;">transcripts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">annotation_dict</span></span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2t_mapping</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="85" 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="LC85" class="line" lang="python">    <span class="n" style="color: #333;">n_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">df_eventalign_index</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">transcripts</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="86" 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="LC86" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n_reads</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">readcount_min</span><span class="p">:</span></span>

</pre>

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

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<td class="new_line diff-line-num" data-linenumber="87" 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="LC87" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">transcripts</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="88" 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="LC128" class="line" lang="python">            <span class="n" style="color: #333;">tx_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ensembl</span><span class="p">.</span><span class="n" style="color: #333;">transcript_sequence</span><span class="p">(</span><span class="n" style="color: #333;">tx</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="88" 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="LC88" class="line" lang="python">            <span class="n" style="color: #333;">tx_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="89" 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="LC89" class="line" lang="python">            <span class="n" style="color: #333;">tx_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">][</span><span class="s" style="color: #d14;">'chr'</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="90" 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="LC90" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tx_seq</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="91" 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="LC91" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="131" 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="LC131" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">interval</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tx</span><span class="p">.</span><span class="n" style="color: #333;">exon_intervals</span><span class="p">:</span></span>

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<td class="old_line diff-line-num old" data-linenumber="132" 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">

132

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<td class="new_line diff-line-num old" data-linenumber="92" 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="LC132" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g_pos</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;">interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">interval</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># Exclude the rims of exons.</span></span>

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<td class="old_line diff-line-num old" data-linenumber="133" 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">

133

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python">                    <span class="n" style="color: #333;">tx_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx</span><span class="p">.</span><span class="n" style="color: #333;">spliced_offset</span><span class="p">(</span><span class="n" style="color: #333;">g_pos</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="92" 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="LC134" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">g_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">interval</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">g_pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">interval</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]):</span> <span class="c1" style="color: #998; font-style: italic;"># Todo: To improve the mapping</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="92" 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="LC92" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">exon_num</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">][</span><span class="s" style="color: #d14;">'exon'</span><span class="p">])):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="93" 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="LC93" class="line" lang="python">                <span class="n" style="color: #333;">g_interval</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">][</span><span class="s" style="color: #d14;">'exon'</span><span class="p">][</span><span class="n" style="color: #333;">exon_num</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="94" 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="LC94" class="line" lang="python">                <span class="n" style="color: #333;">tx_interval</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">][</span><span class="s" style="color: #d14;">'tx_exon'</span><span class="p">][</span><span class="n" style="color: #333;">exon_num</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="95" 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="LC95" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g_pos</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;">g_interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">g_interval</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># Exclude the rims of exons.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="96" 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="LC96" class="line" lang="python">                    <span class="n" style="color: #333;">dis_from_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g_interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" 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="LC97" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">][</span><span class="s" style="color: #d14;">'strand'</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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="98" 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="LC98" class="line" lang="python">                        <span class="n" style="color: #333;">tx_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx_interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dis_from_start</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="99" 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="LC99" class="line" lang="python">                    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">][</span><span class="s" style="color: #d14;">'strand'</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="100" 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="LC100" class="line" lang="python">                        <span class="n" style="color: #333;">tx_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx_interval</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dis_from_start</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="101" 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">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">g_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">g_interval</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">g_interval</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">g_pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">g_interval</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]):</span> <span class="c1" style="color: #998; font-style: italic;"># Todo: To improve the mapping</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">                        <span class="n" style="color: #333;">kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'XXXXX'</span></span>

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<pre style="margin: 0;"> <span id="LC103" 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="LC104" class="line" lang="python">                        <span class="n" style="color: #333;">kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tx_seq</span><span class="p">[</span><span class="n" style="color: #333;">tx_pos</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:</span><span class="n" style="color: #333;">tx_pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>

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<td class="new_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python">                    <span class="n" style="color: #333;">t2g_dict</span><span class="p">[(</span><span class="n" style="color: #333;">tx</span><span class="p"><span class="idiff left">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="p">,</span><span class="n" style="color: #333;">tx_pos</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">tx</span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">contig</span><span class="p">,</span><span class="n" style="color: #333;">gene_id</span><span class="p">,</span><span class="n" style="color: #333;">g_pos</span><span class="p">,</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># tx.contig is chromosome.</span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python">            <span class="n" style="color: #333;">tx_ids</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p"><span class="idiff left">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">id</span></span><span class="p">]</span></span>

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<td class="old_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="105" 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="LC105" class="line" lang="python">                    <span class="n" style="color: #333;">t2g_dict</span><span class="p">[(</span><span class="n" style="color: #333;">tx</span><span class="p">,</span><span class="n" style="color: #333;">tx_pos</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">tx<span class="idiff left right">_</span>contig</span><span class="p">,</span><span class="n" style="color: #333;">gene_id</span><span class="p">,</span><span class="n" style="color: #333;">g_pos</span><span class="p">,</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># tx.contig is chromosome.</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">            <span class="n" style="color: #333;">tx_ids</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">tx</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">                </span>

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<td class="new_line diff-line-num" data-linenumber="109" 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="LC109" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">n_reads</span><span class="p">,</span> <span class="n" style="color: #333;">tx_ids</span><span class="p">,</span> <span class="n" style="color: #333;">t2g_dict</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="135" 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">@@ -168,7 +135,8 @@ def combine(events_str):</td>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python">        <span class="n" style="color: #333;">eventalign_result</span><span class="p">.</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">inplace</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="LC136" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="137" 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="LC137" class="line" lang="python"></span>

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<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="138" 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="LC171" class="line" lang="python">        <span class="n" style="color: #333;">eventalign_result</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">contig</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">eventalign_result</span><span class="p">[</span><span class="s" style="color: #d14;">'contig'</span><span class="p">]]</span>    <span class="c1" style="color: #998; font-style: italic;">#### CHANGE MADE ####</span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        eventalign_result['transcript_id'] = [contig.split('.')[0] for contig in eventalign_result['contig']]    #### CHANGE MADE ####</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="139" 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="LC139" class="line" lang="python">        <span class="n" style="color: #333;">eventalign_result</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">contig</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">eventalign_result</span><span class="p">[</span><span class="s" style="color: #d14;">'contig'</span><span class="p">]]</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#eventalign_result['transcript_id'] = eventalign_result['contig']</span></span>

</pre>

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

</pre>

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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python">        <span class="n" style="color: #333;">eventalign_result</span><span class="p">[</span><span class="s" style="color: #d14;">'transcriptomic_position'</span><span class="p">]</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;">to_numeric</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_result</span><span class="p">[</span><span class="s" style="color: #d14;">'position'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="c1" style="color: #998; font-style: italic;"># the middle position of 5-mers.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" 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">@@ -189,7 +157,106 @@ def combine(events_str):</td>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">        <span class="n" style="color: #333;">np_events</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;">rec</span><span class="p">.</span><span class="n" style="color: #333;">fromrecords</span><span class="p">(</span><span class="n" style="color: #333;">df_events</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 class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">df_events</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np_events</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="160" 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="LC192" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parallel_preprocess_gene</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;">ensembl</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">,</span><span class="n" style="color: #333;">readcount_max</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="160" 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="LC160" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readFasta</span><span class="p">(</span><span class="n" style="color: #333;">transcript_fasta</span><span class="p">,</span><span class="n" style="color: #333;">is_gff</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="161" 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="LC161" class="line" lang="python">    <span class="n" style="color: #333;">fasta</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;">transcript_fasta</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="162" 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="LC162" class="line" lang="python">    <span class="n" style="color: #333;">entries</span><span class="p">,</span><span class="n" style="color: #333;">separate_by_pipe</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="163" 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="LC163" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ln</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="164" 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="LC164" class="line" lang="python">        <span class="n" style="color: #333;">entries</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ln</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="165" 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="LC165" class="line" lang="python">    <span class="n" style="color: #333;">entries</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">entries</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="166" 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="LC166" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"|"</span><span class="p">))</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="167" 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">

167

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">        <span class="n" style="color: #333;">separate_by_pipe</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="168" 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">

168

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">    <span class="nb" style="color: #0086b3;">dict</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="169" 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">

169

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="170" 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">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python">        <span class="n" style="color: #333;">entry</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="171" 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">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">())</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="172" 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">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python">            <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="173" 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">

173

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python">            <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="174" 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">

174

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC174" class="line" lang="python">            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">seq</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

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

175

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC175" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="176" 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">

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">separate_by_pipe</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="177" 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">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python">                    <span class="n" style="color: #333;">g_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="178" 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">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="179" 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">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python">                    <span class="n" style="color: #333;">g_id</span><span class="o" style="font-weight: 600;">=</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"gene:"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="180" 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">

180

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC180" class="line" lang="python">                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">g_id</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="181" 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">

181

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC181" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">dict</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="182" 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">

182

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="193" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="183" 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">

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readAnnotation</span><span class="p">(</span><span class="n" style="color: #333;">gtf_or_gff</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="184" 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">

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python">    <span class="n" style="color: #333;">gtf</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;">gtf_or_gff</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="185" 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">

185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python">    <span class="nb" style="color: #0086b3;">dict</span><span class="p">,</span><span class="n" style="color: #333;">is_gff</span><span class="o" style="font-weight: 600;">=</span><span class="p">{},</span><span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="186" 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">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ln</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gtf</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="187" 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">

187

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<pre style="margin: 0;">+<span id="LC187" 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;">ln</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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="188" 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">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python">            <span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ln</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="189" 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">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="190" 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">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"ID"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"Parent"</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python">                    <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="192" 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="LC192" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="193" 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="LC193" class="line" lang="python">                    <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="194" 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">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transcript"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="196" 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="LC196" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="197" 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">

197

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python">                    <span class="n" style="color: #333;">attrList</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

198

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python">                    <span class="n" style="color: #333;">attrDict</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrList</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python">                        <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">k</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="202" 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="LC202" class="line" lang="python">                            <span class="n" style="color: #333;">attrDict</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="203" 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="LC203" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;">##tx_id=ln[-1].split('; transcript_id "')[1].split('";')[0]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="204" 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="LC204" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;">##g_id=ln[-1].split('gene_id "')[1].split('";')[0]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="205" 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="LC205" class="line" lang="python">                    <span class="n" style="color: #333;">tx_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attrDict</span><span class="p">[</span><span class="s" style="color: #d14;">"transcript_id"</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="206" 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="LC206" class="line" lang="python">                    <span class="n" style="color: #333;">g_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attrDict</span><span class="p">[</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'chr'</span><span class="p">:</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span><span class="s" style="color: #d14;">'g_id'</span><span class="p">:</span><span class="n" style="color: #333;">g_id</span><span class="p">,</span><span class="s" style="color: #d14;">'strand'</span><span class="p">:</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="209" 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="LC209" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">]:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transcript"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="211" 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="LC211" class="line" lang="python">                                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="212" 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="LC212" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="213" 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="LC213" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="214" 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="LC214" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">]:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="215" 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="LC215" class="line" lang="python">                                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">)]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="216" 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="LC216" class="line" lang="python">                            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="217" 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="LC217" class="line" lang="python">                                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="219" 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="LC219" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"exon"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"mRNA"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="220" 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="LC220" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="221" 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="LC221" class="line" lang="python">                    <span class="n" style="color: #333;">tx_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'transcript:'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">';'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="222" 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="LC222" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"mRNA"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="223" 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="LC223" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"transcript"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="225" 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="LC225" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'chr'</span><span class="p">:</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span><span class="s" style="color: #d14;">'strand'</span><span class="p">:</span><span class="n" style="color: #333;">ln</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="226" 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="LC226" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transcript"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="227" 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="LC227" class="line" lang="python">                            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="228" 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="LC228" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="229" 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="LC229" class="line" lang="python">                            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">)]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="230" 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="LC230" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="231" 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="LC231" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transcript"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="232" 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="LC232" class="line" lang="python">                            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="233" 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="LC233" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="234" 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="LC234" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python">                                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">)]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="236" 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="LC236" class="line" lang="python">                            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="237" 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="LC237" class="line" lang="python">                                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="nb" style="color: #0086b3;">type</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="238" 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="LC238" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#convert genomic positions to tx positions</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="239" 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="LC239" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="240" 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="LC240" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="241" 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="LC241" class="line" lang="python">            <span class="n" style="color: #333;">tx_pos</span><span class="p">,</span><span class="n" style="color: #333;">tx_start</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span><span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="242" 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="LC242" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pair</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">][</span><span class="s" style="color: #d14;">"exon"</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="243" 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="LC243" class="line" lang="python">                <span class="n" style="color: #333;">tx_end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pair</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pair</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tx_start</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="244" 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="LC244" class="line" lang="python">                <span class="n" style="color: #333;">tx_pos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">tx_start</span><span class="p">,</span><span class="n" style="color: #333;">tx_end</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="245" 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="LC245" class="line" lang="python">                <span class="n" style="color: #333;">tx_start</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tx_end</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="246" 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="LC246" class="line" lang="python">            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">][</span><span class="s" style="color: #d14;">'tx_exon'</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tx_pos</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="247" 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="LC247" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="248" 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="LC248" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="249" 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="LC249" class="line" lang="python">            <span class="n" style="color: #333;">tx_pos</span><span class="p">,</span><span class="n" style="color: #333;">tx_start</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span><span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="250" 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="LC250" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">][</span><span class="s" style="color: #d14;">"strand"</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="251" 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="LC251" class="line" lang="python">                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">][</span><span class="s" style="color: #d14;">"exon"</span><span class="p">].</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">tup</span><span class="p">:</span> <span class="n" style="color: #333;">tup</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="252" 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="LC252" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pair</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">][</span><span class="s" style="color: #d14;">"exon"</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="253" 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="LC253" class="line" lang="python">                <span class="n" style="color: #333;">tx_end</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pair</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pair</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tx_start</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="254" 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="LC254" class="line" lang="python">                <span class="n" style="color: #333;">tx_pos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">tx_start</span><span class="p">,</span><span class="n" style="color: #333;">tx_end</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="255" 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="LC255" class="line" lang="python">                <span class="n" style="color: #333;">tx_start</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tx_end</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="256" 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="LC256" class="line" lang="python">            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">][</span><span class="s" style="color: #d14;">'tx_exon'</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tx_pos</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="257" 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="LC257" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">,</span><span class="n" style="color: #333;">is_gff</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="258" 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="LC258" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="259" 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="LC259" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parallel_preprocess_gene</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;">fasta_dict</span><span class="p">,</span><span class="n" style="color: #333;">annotation_dict</span><span class="p">,</span><span class="n" style="color: #333;">is_gff</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">,</span><span class="n" style="color: #333;">readcount_max</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="260" 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="LC260" class="line" lang="python">    </span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="261" 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="LC261" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Create output paths and locks.</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="262" 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="LC262" class="line" lang="python">    <span class="n" style="color: #333;">out_paths</span><span class="p">,</span><span class="n" style="color: #333;">locks</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(),</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -224,22 +291,29 @@ def parallel_preprocess_gene(eventalign_filepath,ensembl,out_dir,n_processes,rea</td>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Get all gene ids and create a dict of eventalign.combine index.</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     gene_ids = set()</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python">    </span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">##add g_id from fasta dict entry if gff annotation is used</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">annotation_dict</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python">                <span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="s" style="color: #d14;">'g_id'</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fasta_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC298" 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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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python">    <span class="n" style="color: #333;">df_eventalign_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="s" style="color: #d14;">'eventalign.index'</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">    <span class="n" style="color: #333;">df_eventalign_index</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">in</span>  <span class="n" style="color: #333;">df_eventalign_index</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]]</span></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    df_eventalign_index['transcript_id'] = [tx_id for tx_id in  df_eventalign_index['transcript_id']]</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python">    <span class="n" style="color: #333;">df_eventalign_index</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">,</span><span class="n" style="color: #333;">inplace</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="LC305" class="line" lang="python">    <span class="n" style="color: #333;">g2t_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">df_eventalign_index</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python">            <span class="n" style="color: #333;">g_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ensembl</span><span class="p">.</span><span class="n" style="color: #333;">transcript_by_id</span><span class="p">(</span><span class="n" style="color: #333;">tx_id</span><span class="p">).</span><span class="n" style="color: #333;">gene_id</span> </span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">##           g_id = ensembl.transcript_by_id(tx_id).gene_id </span></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python">            <span class="n" style="color: #333;">g_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotation_dict</span><span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">][</span><span class="s" style="color: #d14;">'g_id'</span><span class="p">]</span> </span>

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<pre style="margin: 0;">+<span id="LC311" 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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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC313" 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="LC314" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#             gene_ids = gene_ids.union([g_id])</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">            <span class="n" style="color: #333;">g2t_mapping</span><span class="p">[</span><span class="n" style="color: #333;">g_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python">        </span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     f = open(os.path.join(out_dir,'eventalign.index'))</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     for ln in f:</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#         tx_id,read_index,pos_start,pos_end = ln.split(',')</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" 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">@@ -265,7 +339,7 @@ def parallel_preprocess_gene(eventalign_filepath,ensembl,out_dir,n_processes,rea</td>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># mapping a gene <-> transcripts</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python">            <span class="n" style="color: #333;">n_reads</span><span class="p">,</span> <span class="n" style="color: #333;">tx_ids</span><span class="p">,</span> <span class="n" style="color: #333;">t2g_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t2g</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">ensembl</span></span><span class="p">,</span><span class="n" style="color: #333;">g2t_mapping</span><span class="p">,</span><span class="n" style="color: #333;">df_eventalign_index</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python">            <span class="n" style="color: #333;">n_reads</span><span class="p">,</span> <span class="n" style="color: #333;">tx_ids</span><span class="p">,</span> <span class="n" style="color: #333;">t2g_mapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t2g</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left">fasta_dict</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">annotation_dict</span></span><span class="p">,</span><span class="n" style="color: #333;">g2t_mapping</span><span class="p">,</span><span class="n" style="color: #333;">df_eventalign_index</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n_reads</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">readcount_min</span><span class="p">:</span> </span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python">                <span class="n" style="color: #333;">data_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="340" 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">@@ -340,7 +414,7 @@ def preprocess_gene(gene_id,data_dict,t2g_mapping,out_paths,locks):</td>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#         if len(events_per_read) > 0:</span></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># ===== transcript to gene coordinates ===== # TODO: to use gtf.</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        tx_ids = [tx_id.decode('UTF-8').split('.')[0] for tx_id in events_per_read['transcript_id']]</span></span>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python">        <span class="n" style="color: #333;">tx_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tx_id</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">events_per_read</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]]</span> </span>

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<td class="new_line diff-line-num new" data-linenumber="417" 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="LC417" class="line" lang="python">        <span class="n" style="color: #333;">tx_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'.'</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span></span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">events_per_read</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]]</span> </span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python">        <span class="n" style="color: #333;">tx_positions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">events_per_read</span><span class="p">[</span><span class="s" style="color: #d14;">'transcriptomic_position'</span><span class="p">]</span></span>

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<td class="new_line diff-line-num" data-linenumber="419" 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="LC419" class="line" lang="python">        <span class="n" style="color: #333;">genomic_coordinate</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">tx_ids</span><span class="p">,</span><span class="n" style="color: #333;">tx_positions</span><span class="p">))(</span><span class="n" style="color: #333;">t2g_mapping</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># genomic_coordinates -- np structured array of 'chr','gene_id','genomic_position','kmer'</span></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python">        <span class="n" style="color: #333;">genomic_coordinate</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;">array</span><span class="p">(</span><span class="n" style="color: #333;">genomic_coordinate</span><span class="p">,</span><span class="n" style="color: #333;">dtype</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;">dtype</span><span class="p">([(</span><span class="s" style="color: #d14;">'chr'</span><span class="p">,</span><span class="s" style="color: #d14;">'<U2'</span><span class="p">),(</span><span class="s" style="color: #d14;">'gene_id'</span><span class="p">,</span><span class="s" style="color: #d14;">'<U15'</span><span class="p">),(</span><span class="s" style="color: #d14;">'genomic_position'</span><span class="p">,</span><span class="s" style="color: #d14;">'<i4'</span><span class="p">),(</span><span class="s" style="color: #d14;">'g_kmer'</span><span class="p">,</span><span class="s" style="color: #d14;">'<U5'</span><span class="p">)]))</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" 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="470" 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">@@ -396,6 +470,7 @@ def preprocess_gene(gene_id,data_dict,t2g_mapping,out_paths,locks):</td>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python">            </span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g_kmer_array</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g_kmer_array</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;">##to weed out the mapped kmers from tx_seq that contain 'N', which is not in diffmod's model_kmer</span></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="p">{</span><span class="n" style="color: #333;">position</span><span class="p">}</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g_positions_array</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python">            <span class="n" style="color: #333;">asserted</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="459" 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">@@ -459,7 +534,8 @@ def parallel_preprocess_tx(eventalign_filepath,out_dir,n_processes,readcount_min</td>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Load tasks into task_queue.</span></span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">    <span class="n" style="color: #333;">tx_ids_processed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python">    <span class="n" style="color: #333;">df_eventalign_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="s" style="color: #d14;">'eventalign.index'</span><span class="p">))</span></span>

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<td class="new_line diff-line-num old" data-linenumber="537" 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="LC462" class="line" lang="python">    <span class="n" style="color: #333;">df_eventalign_index</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tx_id</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tx_id</span> <span class="ow" style="font-weight: 600;">in</span>  <span class="n" style="color: #333;">df_eventalign_index</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">]]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    df_eventalign_index['transcript_id'] = [tx_id.split('.')[0] for tx_id in  df_eventalign_index['transcript_id']]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="538" 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="LC538" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    df_eventalign_index['transcript_id'] = [tx_id for tx_id in  df_eventalign_index['transcript_id']]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="539" 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="LC539" class="line" lang="python">    <span class="n" style="color: #333;">tx_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df_eventalign_index</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">].</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="540" 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="LC540" class="line" lang="python">    <span class="n" style="color: #333;">tx_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">.</span><span class="n" style="color: #333;">fromkeys</span><span class="p">(</span><span class="n" style="color: #333;">tx_ids</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="541" 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="LC541" class="line" lang="python">    <span class="n" style="color: #333;">df_eventalign_index</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'transcript_id'</span><span class="p">,</span><span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="472" 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="548" 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">@@ -472,7 +548,7 @@ def parallel_preprocess_tx(eventalign_filepath,out_dir,n_processes,readcount_min</td>

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472

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python">                <span class="n" style="color: #333;">eventalign_result</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">pos_start</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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473

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python">                <span class="n" style="color: #333;">events_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">eventalign_result</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">pos_end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pos_start</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="550" 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="LC550" class="line" lang="python">                <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combine</span><span class="p">(</span><span class="n" style="color: #333;">events_str</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="551" 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="LC475" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="551" 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">

551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">is</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="476" 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">

476

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<td class="new_line diff-line-num" data-linenumber="552" 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="LC552" class="line" lang="python">                    <span class="n" style="color: #333;">data_dict</span><span class="p">[</span><span class="n" style="color: #333;">read_index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="553" 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="LC553" class="line" lang="python">                <span class="n" style="color: #333;">readcount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="478" 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">

478

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<td class="new_line diff-line-num" data-linenumber="554" 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="LC554" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">readcount</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">readcount_max</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="553" 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="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -553,6 +629,7 @@ def preprocess_tx(tx_id,data_dict,out_paths,locks):</td>

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553

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<td class="new_line diff-line-num" data-linenumber="629" 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="LC629" class="line" lang="python">            </span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="630" 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="LC630" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="631" 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="LC631" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">reference_kmer_array</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="632" 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="LC632" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">reference_kmer_array</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;">##to weed out the mapped kmers from tx_seq that contain 'N', which is not in diffmod's model_kmer</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="556" 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">

556

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<td class="new_line diff-line-num" data-linenumber="633" 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="LC633" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="557" 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">

557

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<td class="new_line diff-line-num" data-linenumber="634" 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="LC634" class="line" lang="python">            <span class="n" style="color: #333;">asserted</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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558

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<td class="new_line diff-line-num" data-linenumber="635" 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">

635

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -609,59 +686,70 @@ def preprocess_tx(tx_id,data_dict,out_paths,locks):</td>

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                     assert row_eventalign['read_index'] == read_index </span></span>

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<pre style="margin: 0;"> <span id="LC687" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                     eventalign_per_read = [row_eventalign]</span></span>

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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC613" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC614" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>

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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_args</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#def check_gene_tx_id_version(gtf_or_gff):</span></span>

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    gtf=open(gtf_or_gff,"r")</span></span>

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    extra_version_fields=0</span></span>

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    for i in range(25):</span></span>

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        ln=gtf.readline().split('\t')</span></span>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        if not ln[0].startswith('#'):</span></span>

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#            if ln[2] == "transcript" or ln[2] == "exon":</span></span>

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                check_transcript_version = len(ln[-1].split('transcript_version')) == 2</span></span>

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                check_gene_version = len(ln[-1].split('gene_version')) == 2</span></span>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                if check_transcript_version and check_gene_version:</span></span>

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                   extra_version_fields+=1</span></span>

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    if extra_version_fields > 0:</span></span>

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701

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        return True</span></span>

</pre>

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702

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    else:</span></span>

</pre>

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703

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<pre style="margin: 0;">+<span id="LC703" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        return False</span></span>

</pre>

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704

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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python"> </span>

</pre>

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705

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#def mergeGTFtxIDversion(gtf_or_gff,out_dir):</span></span>

</pre>

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706

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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    gtf=open(gtf_or_gff,"r")</span></span>

</pre>

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707

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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    new_gtf_path=os.path.join(out_dir,'transcript_id_version_merged.gtf')</span></span>

</pre>

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708

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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    new_gtf=open(new_gtf_path,"w")</span></span>

</pre>

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709

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<pre style="margin: 0;">+<span id="LC709" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    for ln in gtf:</span></span>

</pre>

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710

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<pre style="margin: 0;">+<span id="LC710" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        if not ln.startswith("#"):</span></span>

</pre>

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711

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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#            ln=ln.split("\t")</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="712" 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">

712

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<pre style="margin: 0;">+<span id="LC712" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#            if ln[2] == "transcript" or ln[2] == "exon":</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="713" 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">

713

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<pre style="margin: 0;">+<span id="LC713" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                g_id=ln[-1].split('gene_id "')[1].split('";')[0]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="714" 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">

714

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                g_ver=ln[-1].split('; gene_version "')[1].split('";')[0]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="715" 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">

715

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<pre style="margin: 0;">+<span id="LC715" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                tx_id=ln[-1].split('; transcript_id "')[1].split('";')[0]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="716" 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">

716

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<pre style="margin: 0;">+<span id="LC716" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                tx_ver=ln[-1].split('; transcript_version "')[1].split('";')[0]</span></span>

</pre>

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</td>

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717

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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                new_gtf.write('\t'.join(ln[:-1])+'\t'+'gene_id "'+g_id+'.'+g_ver+'"; transcript_id "'+tx_id+'.'+tx_ver+'";'+'\n')</span></span>

</pre>

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718

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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    new_gtf.close()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="719" 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">

719

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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    return new_gtf_path</span></span>

</pre>

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</td>

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720

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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="616" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="721" 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">

721

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dataprep</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="616" 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">

616

</td>

<td class="new_line diff-line-num" data-linenumber="722" 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">

722

</td>

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

<pre style="margin: 0;"> <span id="LC722" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="617" 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">

617

</td>

<td class="new_line diff-line-num" data-linenumber="723" 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">

723

</td>

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

<pre style="margin: 0;"> <span id="LC723" class="line" lang="python">    <span class="n" style="color: #333;">n_processes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">n_processes</span>        </span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="618" 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">

618

</td>

<td class="new_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

</td>

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

<pre style="margin: 0;"> <span id="LC724" class="line" lang="python">    <span class="n" style="color: #333;">eventalign_filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">eventalign</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="619" 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">

619

</td>

<td class="new_line diff-line-num old" data-linenumber="725" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC619" class="line" lang="python">    <span class="n" style="color: #333;">summary_filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">summary</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="620" 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">

620

</td>

<td class="new_line diff-line-num" data-linenumber="725" 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">

725

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<pre style="margin: 0;"> <span id="LC725" class="line" lang="python">    <span class="n" style="color: #333;">chunk_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">chunk_size</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="621" 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">

621

</td>

<td class="new_line diff-line-num" data-linenumber="726" 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">

726

</td>

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

<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">    <span class="n" style="color: #333;">out_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out_dir</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="622" 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">

622

</td>

<td class="new_line diff-line-num old" data-linenumber="727" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC622" class="line" lang="python">    <span class="n" style="color: #333;">ensembl_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ensembl</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="623" 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">

623

</td>

<td class="new_line diff-line-num old" data-linenumber="727" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC623" class="line" lang="python">    <span class="n" style="color: #333;">ensembl_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">species</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="624" 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">

624

</td>

<td class="new_line diff-line-num" data-linenumber="727" 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">

727

</td>

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

<pre style="margin: 0;"> <span id="LC727" class="line" lang="python">    <span class="n" style="color: #333;">readcount_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">readcount_min</span>    </span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="625" 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">

625

</td>

<td class="new_line diff-line-num" data-linenumber="728" 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">

728

</td>

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

<pre style="margin: 0;"> <span id="LC728" class="line" lang="python">    <span class="n" style="color: #333;">readcount_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">readcount_max</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="626" 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">

626

</td>

<td class="new_line diff-line-num" data-linenumber="729" 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">

729

</td>

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

<pre style="margin: 0;"> <span id="LC729" class="line" lang="python">    <span class="n" style="color: #333;">resume</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">resume</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="627" 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">

627

</td>

<td class="new_line diff-line-num" data-linenumber="730" 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">

730

</td>

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

<pre style="margin: 0;"> <span id="LC730" class="line" lang="python">    <span class="n" style="color: #333;">genome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">genome</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="628" 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">

628

</td>

<td class="new_line diff-line-num" data-linenumber="731" 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">

731

</td>

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

<pre style="margin: 0;"> <span id="LC731" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="629" 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">

629

</td>

<td class="new_line diff-line-num old" data-linenumber="732" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC629" class="line" lang="python">    <span class="n" style="color: #333;">customised_genome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">customised_genome</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="630" 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">

630

</td>

<td class="new_line diff-line-num old" data-linenumber="732" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC630" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">customised_genome</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">reference_name</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">annotation_name</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gtf_path_or_url</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">transcript_fasta_paths_or_urls</span><span class="p">]):</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="631" 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">

631

</td>

<td class="new_line diff-line-num old" data-linenumber="732" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC631" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'If you have your own customised genome not in Ensembl, please provide the following'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="632" 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">

632

</td>

<td class="new_line diff-line-num old" data-linenumber="732" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC632" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'- reference_name'</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="633" 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">

633

</td>

<td class="new_line diff-line-num old" data-linenumber="732" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC633" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'- annotation_name'</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="634" 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">

634

</td>

<td class="new_line diff-line-num old" data-linenumber="732" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC634" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'- gtf_path_or_url'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="635" 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">

635

</td>

<td class="new_line diff-line-num old" data-linenumber="732" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC635" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'- transcript_fasta_paths_or_urls'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="636" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="732" 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">

732

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC732" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">genome</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gtf_or_gff</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">transcript_fasta</span><span class="p">]):</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="636" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="733" 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">

733

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC733" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'please provide the following'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="636" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="734" 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">

734

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC734" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'- gtf_or_gff'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="636" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="735" 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">

735

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC735" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'- transcript_fasta'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="636" 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">

636

</td>

<td class="new_line diff-line-num" data-linenumber="736" 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">

736

</td>

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

<pre style="margin: 0;"> <span id="LC736" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="637" 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">

637

</td>

<td class="new_line diff-line-num old" data-linenumber="737" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC637" class="line" lang="python">        <span class="n" style="color: #333;">reference_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">reference_name</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="638" 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">

638

</td>

<td class="new_line diff-line-num old" data-linenumber="737" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC638" class="line" lang="python">        <span class="n" style="color: #333;">annotation_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">annotation_name</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="639" 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">

639

</td>

<td class="new_line diff-line-num old" data-linenumber="737" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC639" class="line" lang="python">        <span class="n" style="color: #333;">gtf_path_or_url</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gtf_path_or_url</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="640" 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">

640

</td>

<td class="new_line diff-line-num old" data-linenumber="737" 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">

</td>

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

<pre style="margin: 0;">-<span id="LC640" class="line" lang="python">        <span class="n" style="color: #333;">transcript_fasta_paths_or_urls</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">transcript_fasta_paths_or_urls</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="641" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="737" 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">

737

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC737" class="line" lang="python">        <span class="n" style="color: #333;">gtf_or_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gtf_or_gff</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="641" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="738" 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">

738

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC738" class="line" lang="python">        <span class="n" style="color: #333;">transcript_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">transcript_fasta</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="641" 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">

641

</td>

<td class="new_line diff-line-num" data-linenumber="739" 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">

739

</td>

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

<pre style="margin: 0;"> <span id="LC739" class="line" lang="python">        </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="642" 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">

642

</td>

<td class="new_line diff-line-num" data-linenumber="740" 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">

740

</td>

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

<pre style="margin: 0;"> <span id="LC740" class="line" lang="python">    <span class="n" style="color: #333;">misc</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#todo: check every level.</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="643" 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">

643

</td>

<td class="new_line diff-line-num" data-linenumber="741" 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">

741

</td>

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

<pre style="margin: 0;"> <span id="LC741" class="line" lang="python">    </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="644" 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">

644

</td>

<td class="new_line diff-line-num" data-linenumber="742" 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">

742

</td>

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

<pre style="margin: 0;"> <span id="LC742" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># (1) For each read, combine multiple events aligned to the same positions, the results from nanopolish eventalign, into a single event per position.</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC743" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">skip_eventalign_indexing</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="646" 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">

646

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<td class="new_line diff-line-num old" data-linenumber="744" 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="LC646" class="line" lang="python">        <span class="n" style="color: #333;">parallel_index</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left">summary_filepath</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">chunk_size</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="647" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="744" 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">

744

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<pre style="margin: 0;">+<span id="LC744" class="line" lang="python">        <span class="n" style="color: #333;">parallel_index</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;">chunk_size</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="647" 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">

647

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<td class="new_line diff-line-num" data-linenumber="745" 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="LC745" class="line" lang="python">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="746" 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">

746

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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># (2) Create a .json file, where the info of all reads are stored per position, for modelling.</span></span>

</pre>

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649

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<td class="new_line diff-line-num" data-linenumber="747" 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">

747

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<pre style="margin: 0;"> <span id="LC747" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">genome</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="650" 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">

650

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC650" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">customised_genome</span><span class="p">:</span></span>

</pre>

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651

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC651" class="line" lang="python">            <span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Genome</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="652" 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">

652

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC652" class="line" lang="python">                <span class="n" style="color: #333;">reference_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reference_name</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="653" 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">

653

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC653" class="line" lang="python">                <span class="n" style="color: #333;">annotation_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">annotation_name</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC654" class="line" lang="python">                <span class="n" style="color: #333;">gtf_path_or_url</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gtf_path_or_url</span><span class="p">,</span></span>

</pre>

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655

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC655" class="line" lang="python">                <span class="n" style="color: #333;">transcript_fasta_paths_or_urls</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">transcript_fasta_paths_or_urls</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC656" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC657" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># parse GTF and construct database of genomic features</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC658" class="line" lang="python">            <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC659" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="660" 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">

660

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC660" class="line" lang="python">            <span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EnsemblRelease</span><span class="p">(</span><span class="n" style="color: #333;">ensembl_version</span><span class="p">,</span><span class="n" style="color: #333;">ensembl_species</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Default: human reference genome GRCh38 release 91 used in the ont mapping.    </span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC661" class="line" lang="python">        <span class="n" style="color: #333;">parallel_preprocess_gene</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;">db</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">,</span><span class="n" style="color: #333;">readcount_max</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="748" 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="LC662" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="748" 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="LC748" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        merge_transcript_id_version = check_gene_tx_id_version(gtf_or_gff)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC749" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        if merge_transcript_id_version:</span></span>

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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#            gtf_or_gff = mergeGTFtxIDversion(gtf_or_gff,out_dir)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC751" class="line" lang="python">        <span class="n" style="color: #333;">annotation_dict</span><span class="p">,</span><span class="n" style="color: #333;">is_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readAnnotation</span><span class="p">(</span><span class="n" style="color: #333;">gtf_or_gff</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="752" 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="LC752" class="line" lang="python">        <span class="n" style="color: #333;">fasta_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readFasta</span><span class="p">(</span><span class="n" style="color: #333;">transcript_fasta</span><span class="p">,</span><span class="n" style="color: #333;">is_gff</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC753" class="line" lang="python">        <span class="n" style="color: #333;">parallel_preprocess_gene</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;">fasta_dict</span><span class="p">,</span><span class="n" style="color: #333;">annotation_dict</span><span class="p">,</span><span class="n" style="color: #333;">is_gff</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">,</span><span class="n" style="color: #333;">readcount_max</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC754" 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="LC755" class="line" lang="python">        <span class="n" style="color: #333;">parallel_preprocess_tx</span><span class="p">(</span><span class="n" style="color: #333;">eventalign_filepath</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="n" style="color: #333;">n_processes</span><span class="p">,</span><span class="n" style="color: #333;">readcount_min</span><span class="p">,</span><span class="n" style="color: #333;">readcount_max</span><span class="p">,</span><span class="n" style="color: #333;">resume</span><span class="p">)</span></span></pre>

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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="756" 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="LC667" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>

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<br>

</li>

<li id="914848e996270683a7a728dd93078d41e21774e1">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#914848e996270683a7a728dd93078d41e21774e1"><strong>xpore/scripts/diffmod.py</strong></a>

<hr>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>

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<pre style="margin: 0;"> <span id="LC1" 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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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="3" 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="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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="11" 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">@@ -12,25 +11,6 @@ from ..diffmod.configurator import Configurator</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..diffmod.gmm</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GMM</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..diffmod</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">io</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..diffmod.statstest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StatsTest</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC15" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_args</span><span class="p">():</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC17" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentDefaultsHelpFormatter</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC18" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="19" 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="LC19" class="line" lang="python">    <span class="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC20" class="line" lang="python">    <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'required arguments'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC21" class="line" lang="python">    </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC22" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Required arguments</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC23" class="line" lang="python">    <span class="n" style="color: #333;">required</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--config'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'config'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'yaml configuraion filepath.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC24" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Optional arguments</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC26" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'number of processes to run.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="14" 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="LC27" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--save_models'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'save_models'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'with this argument, the program will save the model parameters for each id.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># todo</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--resume'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'resume'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'with this argument, the program will resume from the previous run.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> </span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python">    </span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python">    <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--ids'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ids'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gene / transcript ids to model.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span><span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'*'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">        </span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">execute</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">data_dict</span><span class="p">,</span> <span class="n" style="color: #333;">data_info</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="n" style="color: #333;">criteria</span><span class="p">,</span> <span class="n" style="color: #333;">model_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">prior_params</span><span class="p">,</span> <span class="n" style="color: #333;">out_paths</span><span class="p">,</span> <span class="n" style="color: #333;">save_models</span><span class="p">,</span><span class="n" style="color: #333;">locks</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" 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="76" 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">@@ -96,8 +76,7 @@ def execute(idx, data_dict, data_info, method, criteria, model_kmer, prior_param</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">locks</span><span class="p">[</span><span class="s" style="color: #d14;">'log'</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_paths</span><span class="p">[</span><span class="s" style="color: #d14;">'log'</span><span class="p">],</span><span class="s" style="color: #d14;">'a'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">        <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">idx</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="LC78" class="line" lang="python">                        </span>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_args</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">diffmod</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">    </span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">n_processes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">n_processes</span>       </span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">    <span class="n" style="color: #333;">config_filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">config</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -205,16 +184,6 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Close data files</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f_data</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>

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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="186" 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="LC186" class="line" lang="python">        <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span>   </span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"><span class="idiff left right">        </span></span>

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<td class="old_line diff-line-num new" data-linenumber="209" 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="LC187" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_paths</span><span class="p">[</span><span class="s" style="color: #d14;">'log'</span><span class="p">],</span><span class="s" style="color: #d14;">'a+'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="210" 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="LC189" class="line" lang="python">        <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">helper</span><span class="p">.</span><span class="n" style="color: #333;">decor_message</span><span class="p">(</span><span class="s" style="color: #d14;">'successfully finished'</span><span class="p">))</span></span></pre>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python">        </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;">    Usage:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="216" 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="LC216" class="line" lang="python"><span class="s" style="color: #d14;">        xpore-diffmod --config CONFIG [--n_processes N_PROCESSES] </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;">                     [--save_models] [--resume] </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"><span class="s" style="color: #d14;">                     [--ids [IDS [IDS ...]]]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>

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<br>

</li>

<li id="845edb6ada5749d19a27b846df666a2bb131a9a9">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#845edb6ada5749d19a27b846df666a2bb131a9a9"><strong>xpore/scripts/postprocessing.py</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_postprocessing</span><span class="p">(</span><span class="n" style="color: #333;">diffmod_table_path</span><span class="p">,</span><span class="n" style="color: #333;">out_dir</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python">    <span class="nb" style="color: #0086b3;">file</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;">diffmod_table_path</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python">    <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python">    <span class="n" style="color: #333;">entries</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python">    <span class="n" style="color: #333;">outfile_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">out_dir</span><span class="p">,</span><span class="s" style="color: #d14;">"majority_direction_kmer_diffmod.table"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="n" style="color: #333;">outfile</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;">outfile_path</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">    <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">    <span class="n" style="color: #333;">kmer_ind</span><span class="p">,</span><span class="n" style="color: #333;">dir_ind</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'kmer'</span><span class="p">),</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'mod_assignment'</span><span class="p">)</span>    </span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">    <span class="nb" style="color: #0086b3;">dict</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ln</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">entries</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">        <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ln</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="15" 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="LC15" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">kmer_ind</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">kmer_ind</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">dir_ind</span><span class="p">]:</span><span class="mi" style="color: #099;">1</span><span class="p">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" 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">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">dir_ind</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">kmer_ind</span><span class="p">]]:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">kmer_ind</span><span class="p">]][</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">dir_ind</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" 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">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">kmer_ind</span><span class="p">]][</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">dir_ind</span><span class="p">]]</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" 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">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" 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">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;">##consider one modification type per k-mer</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="s" style="color: #d14;">'higher'</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="s" style="color: #d14;">'lower'</span><span class="p">]:</span> <span class="c1" style="color: #998; font-style: italic;">##choose the majority</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="25" 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">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="s" style="color: #d14;">'choose'</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'lower'</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="26" 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">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="27" 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">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">                <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="s" style="color: #d14;">'choose'</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'higher'</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" 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">

29

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">            <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="s" style="color: #d14;">'choose'</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ln</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">entries</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" 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">

31

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">        <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ln</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="32" 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">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">dir_ind</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">kmer_ind</span><span class="p">]][</span><span class="s" style="color: #d14;">'choose'</span><span class="p">]:</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">            <span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">ln</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="34" 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">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">    <span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="35" 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="LC35" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="36" 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="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">postprocessing</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="37" 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="LC37" class="line" lang="python">    <span class="n" style="color: #333;">diffmod_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">diffmod_dir</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" 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">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">diffmod_table_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">diffmod_dir</span><span class="p">,</span><span class="s" style="color: #d14;">"diffmod.table"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" 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="LC39" class="line" lang="python">    <span class="n" style="color: #333;">run_postprocessing</span><span class="p">(</span><span class="n" style="color: #333;">diffmod_table_path</span><span class="p">,</span><span class="n" style="color: #333;">diffmod_dir</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="40" 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">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span></pre>

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<br>

</li>

<li id="f3c38bd4ea15b9ca3d6bc37bad514c99766dd6b6">

<a href="https://salsa.debian.org/med-team/xpore/-/compare/45d62e12569b4d75d74eaae3000b4724c58b6dee...bea8751ee62ee65ba9720fbfce3f73d3ea59108c#f3c38bd4ea15b9ca3d6bc37bad514c99766dd6b6"><strong>xpore/scripts/xpore.py</strong></a>

<hr>

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<td class="new_line diff-line-num new" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.dataprep</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dataprep</span></span>

</pre>

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</td>

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

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.diffmod</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">diffmod</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.postprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">postprocessing</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="6" 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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="7" 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="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_options</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" 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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>

</pre>

</td>

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

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="s" style="color: #d14;">"""Parses options from the command line """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xpore</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'xpore'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">    <span class="n" style="color: #333;">subparsers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_subparsers</span><span class="p">(</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Running modes'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'{dataprep, diffmod, postprocessing}'</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;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'version'</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'%(prog)s {version}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__version__</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">### RUN MODE "DATAPREP"</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">    <span class="n" style="color: #333;">parser_dataprep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subparsers</span><span class="p">.</span><span class="n" style="color: #333;">add_parser</span><span class="p">(</span><span class="s" style="color: #d14;">'dataprep'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'run mode for preprocessing nanopolish eventalign.txt before differential modification analysis'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="n" style="color: #333;">required_dataprep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'required arguments'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Required arguments</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">    <span class="n" style="color: #333;">required_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--eventalign'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'eventalign'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'eventalign filepath, the output from nanopolish.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">##required.add_argument('--summary', dest='summary', help='eventalign summary filepath, the output from nanopolish.',required=True)</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">    <span class="n" style="color: #333;">required_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--out_dir'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'out_dir'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'output directory.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--gtf_or_gff'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gtf_or_gff'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'GTF or GFF file path.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--transcript_fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'transcript_fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'transcript FASTA path.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Optional arguments</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--skip_eventalign_indexing'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'skip_eventalign_indexing'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'skip indexing the eventalign nanopolish output.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--features', dest='features', help='Signal features to extract.',type=list,default=['norm_mean'])</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--genome'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'genome'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'to run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> </span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'number of processes to run.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</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;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--chunk_size'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'chunk_size'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'number of lines from nanopolish eventalign.txt for processing.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000000</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;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--readcount_min'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'readcount_min'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'minimum read counts per gene.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--readcount_max'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'readcount_max'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'maximum read counts per gene.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">    <span class="n" style="color: #333;">optional_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--resume'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'resume'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'with this argument, the program will resume from the previous run.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#todo</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">    <span class="n" style="color: #333;">parser_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">optional_dataprep</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">parser_dataprep</span><span class="p">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dataprep</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">### RUN MODE "DIFFMOD"</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">    <span class="n" style="color: #333;">parser_diffmod</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subparsers</span><span class="p">.</span><span class="n" style="color: #333;">add_parser</span><span class="p">(</span><span class="s" style="color: #d14;">'diffmod'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'run mode for performing differential modification analysis'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">    <span class="n" style="color: #333;">optional_diffmod</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">    <span class="n" style="color: #333;">required_diffmod</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'required arguments'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Required arguments</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">    <span class="n" style="color: #333;">required_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--config'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'config'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'YAML configuraion filepath.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Optional arguments</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python">    <span class="n" style="color: #333;">optional_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'n_processes'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'number of processes to run.'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</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;">optional_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--save_models'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'save_models'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'with this argument, the program will save the model parameters for each id.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># todo</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">    <span class="n" style="color: #333;">optional_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--resume'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'resume'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'with this argument, the program will resume from the previous run.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">)</span> </span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">    <span class="n" style="color: #333;">optional_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--ids'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ids'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gene or transcript ids to model.'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span><span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'*'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">    <span class="n" style="color: #333;">parser_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">_action_groups</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">optional_diffmod</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;">parser_diffmod</span><span class="p">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">diffmod</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">### RUN MODE "POSTPROCESSING"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">    <span class="n" style="color: #333;">parser_postprocessing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subparsers</span><span class="p">.</span><span class="n" style="color: #333;">add_parser</span><span class="p">(</span><span class="s" style="color: #d14;">'postprocessing'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'run mode for post-processing diffmod.table, the result table from differential modification analysis.'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">    <span class="n" style="color: #333;">required_postprocessing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser_postprocessing</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'required arguments'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Required arguments</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" 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="LC58" class="line" lang="python">    <span class="n" style="color: #333;">required_postprocessing</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--diffmod_dir'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diffmod_dir'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diffmod directory path, the output from xpore-diffmod.'</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="59" 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="LC59" class="line" lang="python">    <span class="n" style="color: #333;">parser_postprocessing</span><span class="p">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">postprocessing</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="60" 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="LC60" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="62" 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="LC62" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="63" 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="LC63" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="64" 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="LC64" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">### get command line options</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="66" 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="LC66" class="line" lang="python">    <span class="n" style="color: #333;">options</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_options</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="67" 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="LC67" class="line" lang="python">    <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">func</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="68" 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="LC68" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="69" 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="LC69" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="70" 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="LC70" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span></span></pre>

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