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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mirtop">Debian Med / mirtop</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1">7cde033d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-15T16:13:25+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.4.24</pre>
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<h4>14 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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−
.travis.yml
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<li class="file-stats">
<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360">
HISTORY.md
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<li class="file-stats">
<a href="#08030f26ac5b9f74ec217abdac2b8fe3fb0ae7e1">
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data/examples/annotate/SQL_sample.gff
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<li class="file-stats">
<a href="#a9e0c5abd611157a2d6fb457e24c28dfb68102d0">
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+
data/examples/annotate/miRNA_sample_list.txt
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<a href="#6dc287cbfb49fb175c2e84f9656a3af0302a6f3e">
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data/examples/annotate/query_sample.db
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<li class="file-stats">
<a href="#7d3898ab9aa7bf41691cac12635467fd32548a0e">
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+
docs/sql_usage.md
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<li class="file-stats">
<a href="#6d064d69ffb7b0c563106b71f75b2cc667c1d3a3">
mirtop/bam/filter.py
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<li class="file-stats">
<a href="#d04a45c446a37e2475ffe20e88836cb40ca9f4b5">
mirtop/command_line.py
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<li class="file-stats">
<a href="#306f6d44363853ea5854c519950a9faaaf5d3ade">
mirtop/libs/parse.py
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<a href="#27410ad28c824687ba85a7f875c5934e7cac0aea">
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mirtop/sql/__init__.py
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<a href="#e8f74686ecc23024f87d8fb213e2853d224e36f7">
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mirtop/sql/sql.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#d0647faf8b4f761b838cd192919a47664375a4cd">
test/test_automated_analysis.py
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<li class="file-stats">
<a href="#0bf568057b7d974795fdf77eef231e1fe43a58b4">
test/test_functions.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</span></span>
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<td class="new_line diff-line-num old" data-linenumber="0" 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="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" 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="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" 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">
6
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">2.7"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="9" 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">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">recipients</span><span class="pi">:</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">lorena.pantano@gmail.com</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">always</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">echo $TRAVIS_PYTHON_VERSION</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">miniconda="Miniconda3-latest-Linux-x86_64.sh"</span></span>
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<td class="old_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="LC15" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [[ $TRAVIS_PYTHON_VERSION == "2.7" ]] ; then miniconda="Miniconda2-latest-Linux-x86_64.sh"; fi</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">wget -O miniconda.sh http://repo.continuum.io/miniconda/${miniconda}</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">bash miniconda.sh -b -p ~/install</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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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="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">export PATH=~/install/bin/:$PATH</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">conda install --yes ncurses -c conda-forge</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">conda install --yes -c conda-forge -c bioconda bedtools samtools razers3 pip nose pysam pandas pyyaml pybedtools biopython setuptools codecov -q</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py develop</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">nosetests --with-coverage</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"><span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">codecov</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">deploy</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypi</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">lpantano</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">secure</span><span class="pi">:</span> <span class="s" style="color: #d14;">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</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_existing</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_BRANCH =~ ^master|dev$</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">distributions</span><span class="pi">:</span> <span class="s" style="color: #d14;">sdist bdist_wheel</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">repo</span><span class="pi">:</span> <span class="s" style="color: #d14;">miRTop/mirtop</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#d30b04166486087de34ff05cf278d3dd2ddd2360"><strong>HISTORY.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="p">-</span> 0.4.23</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="p">0.</span>4.24</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">fix bad</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/miRTop/mirtop/issues/64</span><span class="p">)</span> annotation when 5 or more T/A at the end of the sequence by @DrHogart</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">*</span> Add SQL database creation</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">0.</span>4.23</span>
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2
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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3
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">*</span> fix empty stats file <span class="p">[</span><span class="nv" style="color: #008080;">#61</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/miRTop/mirtop/issues/61</span><span class="p">)</span> by @leontienvdbent</span>
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4
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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5
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<td class="new_line diff-line-num old" data-linenumber="10" 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="LC5" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.4.22</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">0.</span>4.22</span>
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6
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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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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7
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<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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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p">*</span> fix when reads map halfway on to the edge</span>
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8
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<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
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">*</span> fix edge case where limit==variant_size </span>
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9
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
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10
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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="LC10" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.4.21</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">0.</span>4.21</span>
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11
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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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">
12
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p">*</span> Missing trimming events since 0.4.19</span>
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13
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<td class="new_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
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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14
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<td class="new_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="LC14" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.4.20</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">0.</span>4.20</span>
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15
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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16
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">*</span> Support export isomiR rawData output</span>
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17
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<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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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p">*</span> Support genomic coordinates as output in the gff</span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,12 +24,12 @@</td>
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19
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">*</span> Implement method to create gff line</span>
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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">
20
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="p">*</span> Improve docs</span>
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21
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.4.19</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">0.</span>4.19</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"><span class="p">*</span> Add --version option</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="p">*</span> Fix bug that ignore sequences starting at 0 in bam files </span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.4.18</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">0.</span>4.18</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="p"> *</span> Cast map object to list to avoid errors in py3.</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="p"> *</span> Support Manatee output.</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">@@ -52,7 +57,8 @@</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="p"> *</span> Add class to parse GFF line as a first move toward isolation</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="p"> *</span> Add JSON log for stats command.</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"><span class="p">-</span> 0.3.17</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="p">0.</span>3.17</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="p"> *</span> Normalize the read of the tool outputs.</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"><span class="p"> *</span> Add docs with autodoc plugin.</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="p"> *</span> Validator by @Vbarrera.</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">@@ -78,7 +84,7 @@</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"><span class="p"> *</span> Improve PROST! importer</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"><span class="p"> *</span> Fix output for isomiRs package</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.2.<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="p">0.</span>2.<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"><span class="p"> *</span> Make GTF default output</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p"> *</span> Add function to get SNPs from Variant attribute</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +97,7 @@</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"><span class="p"> *</span> Improve isomiR reading from srnabench tool</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"><span class="p"> *</span> Add PROST to supported tools</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.1.7</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="p">0.</span>1.7</span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"><span class="p"> *</span> Remove deletion from addition isomiRs</span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"><span class="p"> *</span> Support for srnabench output</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">@@ -100,14 +106,14 @@</td>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown"><span class="p"> *</span> Functin to guess database used from GTF file through --mirna parameter</span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"><span class="p"> *</span> Adapt output format to https://github.com/miRTop/incubator/blob/master/format/definition.md</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.1.5</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"><span class="p">0.</span>1.5</span>
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104
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>
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105
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="p"> *</span> add function to check correct annotation</span>
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106
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"><span class="p"> *</span> add test data for SAM parsing</span>
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107
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="p"> *</span> add script to simulate isomiRs</span>
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108
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"><span class="p"> *</span> parse indels from bam file</span>
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109
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff right"> </span>0.1.4</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="p">0.</span>1.4</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"><span class="p"> *</span> fix index BAM file command line</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"><span class="p"> *</span> add function to accept indels and test unit</span>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#08030f26ac5b9f74ec217abdac2b8fe3fb0ae7e1"><strong>data/examples/annotate/SQL_sample.gff</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># GFF3 adapted for miRNA sequencing data</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">## VERSION 0.0.1</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## source-ontology: miRBase22</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">## COLDATA: SRR333680_1</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">hsa-miR-342-3p miRBase22 isomiR 61 85 . + . Read TCTCACAAAGAAATCGCACCCGTTC; UID 0t@TeV#5v2; Name hsa-miR-342-3p; Parent hsa-mir-342; Variant iso_snv,iso_add:+2; Cigar 7MA15MTC; Expression 1; Filter Pass</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">hsa-let-7i-5p miRBase22 isomiR 6 28 . + . Read TGAGGTAGTAGTTTGTGCTGTTG; UID 7AwwRIB71; Name hsa-let-7i-5p; Parent hsa-let-7i; Variant iso_3p:+1; Cigar 23M; Expression 1; Filter Pass</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">hsa-miR-10400-5p miRBase22 isomiR 2 21 . + . Read GGCGGCGGCGACTCTGGACT; UID MMM80Kr1; Name hsa-miR-10400-5p; Parent hsa-mir-10400; Variant iso_snvcentral_supp,iso_5p:-1; Cigar 10MA6MAMT; Expression 1; Filter Pass</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">hsa-let-7i-5p miRBase22 isomiR 6 28 . + . Read TGAGGTAGTAGTTTGTGCTGTTA; UID 7AwwRIBL1; Name hsa-let-7i-5p; Parent hsa-let-7i; Variant iso_add:+1; Cigar 22MA; Expression 27; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">hsa-let-7i-5p miRBase22 isomiR 6 28 . + . Read TGAGGTAGTAGTTTGTGCTGTTC; UID 7AwwRIBU1; Name hsa-let-7i-5p; Parent hsa-let-7i; Variant iso_add:+1; Cigar 22MC; Expression 16; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">hsa-miR-320a-3p miRBase22 isomiR 42 67 . + . Read AAAAGCTGGGTTGAGAGGGCGATAAT; UID @ku54hZgg1; Name hsa-miR-320a-3p; Parent hsa-mir-320a; Variant iso_add:+4; Cigar 22MT2MT; Expression 1; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">hsa-miR-99b-5p miRBase22 isomiR 7 24 . + . Read CACCCGTAGAACCGCCCT; UID tyJfEi; Name hsa-miR-99b-5p; Parent hsa-mir-99b; Variant iso_snv,iso_3p:-4; Cigar 14MC3M; Expression 1; Filter Pass</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">hsa-let-7i-5p miRBase22 isomiR 6 28 . + . Read TGAGGTAGTAGTTTGTGCTGTTT; UID 7AwwRIBQ1; Name hsa-let-7i-5p; Parent hsa-let-7i; Variant iso_add:+1; Cigar 22MT; Expression 261; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">hsa-miR-146a-5p miRBase22 isomiR 21 45 . + . Read TGAGAACTGAATTCCATGGGTTGAT; UID 7Tqo9bA7L2; Name hsa-miR-146a-5p; Parent hsa-mir-146a; Variant iso_add:+3; Cigar 23MAT; Expression 3; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">hsa-miR-449c-5p.SNPC miRBase22 isomiR 18 44 . + . Read AGGCAGTGTATTGCTAGCGGCTGGTCG; UID hDBp6kMuP; Name hsa-miR-449c-5p.SNPC; Parent hsa-mir-449c; Variant iso_snv,iso_add:+3,iso_5p:-1; Cigar 23MGMCG; Expression 1; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">hsa-miR-140-3p miRBase22 isomiR 63 86 . + . Read ACCACAGGGTAGAAACACGGATTC; UID al$J@tKO; Name hsa-miR-140-3p; Parent hsa-mir-140; Variant iso_snv,iso_add:+4,iso_5p:-1; Cigar 14MA6MTTC; Expression 1; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">hsa-miR-221-3p miRBase22 isomiR 65 91 . + . Read AGCTACATTGTCTGCTGGGTTTCTTGT; UID kNpYIu50B; Name hsa-miR-221-3p; Parent hsa-mir-221; Variant iso_add:+4; Cigar 23MTTMT; Expression 1; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">hsa-miR-92b-3p miRBase22 isomiR 61 84 . + . Read TATTGCACTCGTCCCGGCCTACAT; UID zIsS#Mrn; Name hsa-miR-92b-3p; Parent hsa-mir-92b; Variant iso_snv,iso_add:+2; Cigar 20MAMAT; Expression 1; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">hsa-miR-1269b.SNPA miRBase22 isomiR 9 27 . + . Read CTGGACTGAGCCATGCTAC; UID q87Xbrv2; Name hsa-miR-1269b.SNPA; Parent hsa-mir-1269b; Variant iso_3p:-3; Cigar 19M; Expression 1; Filter Pass</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">hsa-miR-371a-5p miRBase22 isomiR 6 30 . + . Read ACTCAACCTGTGGGGGCACTTTTTC; UID svi3$VH%v2; Name hsa-miR-371a-5p; Parent hsa-mir-371a; Variant iso_snv_central,iso_add:+5; Cigar 6MC15MTMC; Expression 1; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">hsa-miR-142-5p miRBase22 isomiR 16 36 . + . Read CATAAAGTAGAAAGCACTATC; UID n@WTkse; Name hsa-miR-142-5p; Parent hsa-mir-142; Variant iso_snv; Cigar 19MTC; Expression 5; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">hsa-miR-371a-5p miRBase22 isomiR 6 25 . + . Read GCTCAAACTGTGGGGGCACA; UID 6vs3$Vv1; Name hsa-miR-371a-5p; Parent hsa-mir-371a; Variant iso_snv_seed; Cigar G18MA; Expression 1; Filter Pass</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="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="plaintext">hsa-miR-30e-3p miRBase22 isomiR 59 84 . + . Read CTTTCAGTCGGATGTTTACATCGTAT; UID HUYKBQnSg1; Name hsa-miR-30e-3p; Parent hsa-mir-30e; Variant iso_snv,iso_add:+4; Cigar 20MT2MTAT; Expression 1; Filter Pass</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="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="plaintext">hsa-miR-6727-5p miRBase22 isomiR 8 26 . + . Read TGGGGCAAGCGGCTGGCTC; UID uMcGq6v2; Name hsa-miR-6727-5p; Parent hsa-mir-6727; Variant iso_snv_central_offset,iso_5p:-2,iso_3p:-2; Cigar T6MA8MCTC; Expression 1; Filter Pass</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="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="plaintext">hsa-miR-185-5p miRBase22 isomiR 15 37 . + . Read TGGAGAGAAAGGCAGTTCCTGTC; UID umThDOqU1; Name hsa-miR-185-5p; Parent hsa-mir-185; Variant iso_snv,iso_add:+1; Cigar 21MTC; Expression 1; Filter Pass</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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">hsa-miR-21-5p miRBase22 isomiR 8 24 . + . Read NAGCTTATCAGACTGAT; UID .; Name hsa-miR-21-5p; Parent hsa-mir-21; Variant iso_snv_central_offset,iso_3p:-5; Cigar N16M; Expression 1; Filter Pass</span>
</pre>
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<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="plaintext">hsa-miR-371a-5p miRBase22 isomiR 6 25 . + . Read GCTCAAACTGTGGGGGCACT; UID 6vs3$Vr1; Name hsa-miR-371a-5p; Parent hsa-mir-371a; Variant iso_snv_seed; Cigar G19M; Expression 3; Filter Pass</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="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="plaintext">hsa-miR-372-3p miRBase22 isomiR 42 65 . + . Read AAAGTGCTGCGACATTTGAGCGGT; UID @3qCnRkA; Name hsa-miR-372-3p; Parent hsa-mir-372; Variant iso_snv,iso_add:+1; Cigar 22MGT; Expression 1; Filter Pass</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="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="plaintext">hsa-miR-371a-5p miRBase22 isomiR 6 28 . + . Read ACTCAAACTGTGGGGGCTTTTCG; UID svs3$6%C1; Name hsa-miR-371a-5p; Parent hsa-mir-371a; Variant iso_snv,iso_add:+3; Cigar 17MTT2MCG; Expression 1; Filter Pass</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="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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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">hsa-miR-127-3p miRBase22 isomiR 57 83 . + . Read TCGGATCCGTCTGAGCTTGGCTGTCGT; UID PFy04HMBS; Name hsa-miR-127-3p; Parent hsa-mir-127; Variant iso_add:+5; Cigar 23MTCGT; Expression 1; Filter Pass</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="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="plaintext">hsa-let-7e-5p miRBase22 isomiR 8 32 . + . Read NGAGGTAGGAGGTTGTATAGTTCGT; UID .; Name hsa-let-7e-5p; Parent hsa-let-7e; Variant iso_snv_central_offset,iso_add:+3; Cigar N21MCGT; Expression 4; Filter Pass</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="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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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">hsa-miR-409-3p miRBase22 isomiR 45 64 . + . Read ACGAATGTTGCTCGGTGAAT; UID do56G7g1; Name hsa-miR-409-3p; Parent hsa-mir-409; Variant iso_snv,iso_5p:+2,iso_3p:-4; Cigar 19MT; Expression 1; Filter Pass</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="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="plaintext">hsa-miR-509-3-5p miRBase22 isomiR 10 26 . + . Read TACTGCCGACGTGGCAA; UID NICSM@1; Name hsa-miR-509-3-5p; Parent hsa-mir-509-3; Variant iso_snvcentral_supp,iso_3p:-5; Cigar 6MC10M; Expression 1; Filter Pass</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="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
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">hsa-let-7c-5p miRBase22 isomiR 12 35 . + . Read GAGGTAGTAGGTTGTATGGTTCCG; UID 4WWABb5y; Name hsa-let-7c-5p; Parent hsa-let-7c; Variant iso_add:+3,iso_5p:-1; Cigar 21MCCM; Expression 1; Filter Pass</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="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="plaintext">hsa-miR-99b-3p miRBase22 isomiR 45 62 . + . Read CAAGCTCGTGTCTGTGGG; UID v6SYB$; Name hsa-miR-99b-3p; Parent hsa-mir-99b; Variant iso_3p:-4; Cigar 18M; Expression 2; Filter Pass</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="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">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">hsa-miR-30a-5p miRBase22 isomiR 7 28 . + . Read GTAAACATCCTCGACTGGAAGC; UID Wfej8ucv2; Name hsa-miR-30a-5p; Parent hsa-mir-30a; Variant iso_5p:-1,iso_3p:+1; Cigar 22M; Expression 1; Filter Pass</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="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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">hsa-miR-140-3p miRBase22 isomiR 62 86 . + . Read TACCACAGGGTAGAACCCCGGAAAT; UID NthWT#G@L2; Name hsa-miR-140-3p; Parent hsa-mir-140; Variant iso_snv,iso_add:+4; Cigar 17MC4MAMT; Expression 1; Filter Pass</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="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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">hsa-miR-382-3p miRBase22 isomiR 47 69 . + . Read AATCATTCACGGACAACACTTCG; UID onUGllHC1; Name hsa-miR-382-3p; Parent hsa-mir-382; Variant iso_add:+2; Cigar 21MCG; Expression 2; Filter Pass</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="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="plaintext">hsa-miR-127-3p miRBase22 isomiR 57 84 . + . Read TCGGATCCGTCTGAGCTTGGCTTTTCGT; UID PFy04HM%PL2; Name hsa-miR-127-3p; Parent hsa-mir-127; Variant iso_add:+6; Cigar 22MTT3MT; Expression 1; Filter Pass</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="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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">hsa-miR-372-3p miRBase22 isomiR 43 61 . + . Read AAGTGCTGCGACAGTTGAG; UID cII8w7T2; Name hsa-miR-372-3p; Parent hsa-mir-372; Variant iso_snv,iso_5p:-1,iso_3p:-3; Cigar 13MG5M; Expression 1; Filter Pass</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">
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">hsa-let-7f-5p miRBase22 isomiR 7 28 . + . Read TGAGGTAGTAGATTGTATTGTT; UID 7AwmRzBL2; Name hsa-let-7f-5p; Parent hsa-let-7f-1; Variant iso_snv; Cigar 18MT3M; Expression 1; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="plaintext">hsa-miR-145-5p miRBase22 isomiR 16 40 . + . Read GTCCAGTTTTCCCAGGAATCCCTCG; UID YD%9DT9jT2; Name hsa-miR-145-5p; Parent hsa-mir-145; Variant iso_add:+2; Cigar 23MCG; Expression 2; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="plaintext">hsa-miR-99b-5p miRBase22 isomiR 7 25 . + . Read CACCCGTAGAACCGACCTT; UID tyJfCiL2; Name hsa-miR-99b-5p; Parent hsa-mir-99b; Variant iso_3p:-3; Cigar 19M; Expression 14; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="plaintext">hsa-miR-26a-5p miRBase22 isomiR 11 30 . + . Read TCAAGTAATCCAGGATAGGC; UID UwoxKJV1; Name hsa-miR-26a-5p; Parent hsa-mir-26a-1; Variant iso_5p:-1,iso_3p:-1; Cigar 20M; Expression 3; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">hsa-miR-99b-5p miRBase22 isomiR 7 27 . + . Read CACCCGTAGAACCGACCTTGC; UID tyJfCiI; Name hsa-miR-99b-5p; Parent hsa-mir-99b; Variant iso_3p:-1; Cigar 21M; Expression 3; Filter Pass</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="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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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">hsa-miR-371a-5p miRBase22 isomiR 6 25 . + . Read ACTCAAACTGTGGGGGAACT; UID svs3$Tr1; Name hsa-miR-371a-5p; Parent hsa-mir-371a; Variant iso_snv; Cigar 16MA3M; Expression 26; Filter Pass</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">hsa-miR-371a-5p miRBase22 isomiR 6 29 . + . Read ACTAAAACTGTGGGGGCACTTTAG; UID s@s3$VHJ; Name hsa-miR-371a-5p; Parent hsa-mir-371a; Variant iso_snv_central,iso_add:+4; Cigar 3MA18MAG; Expression 1; Filter Pass</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="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="plaintext">hsa-miR-140-3p miRBase22 isomiR 62 86 . + . Read TACCACAGGGTAGAACCACGGCTCG; UID NthWTxGjT2; Name hsa-miR-140-3p; Parent hsa-mir-140; Variant iso_add:+4; Cigar 21MCTCM; Expression 2; Filter Pass</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="48" style="width: 35px; color: rgba(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="LC48" class="line" lang="plaintext">hsa-miR-6765-5p miRBase22 isomiR 15 30 . + . Read CGCGGGTCTGTGGCGC; UID E$03Zv2; Name hsa-miR-6765-5p; Parent hsa-mir-6765; Variant iso_snvcentral_supp,iso_add:+5,iso_5p:-14; Cigar CMC4MC7MC; Expression 1; Filter Pass</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="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="plaintext">hsa-miR-5010-5p miRBase22 isomiR 23 50 . + . Read GGGGATGGCAGAGCAAAATTCATGGCTC; UID $FMmV@Ob6v2; Name hsa-miR-5010-5p; Parent hsa-mir-5010; Variant iso_add:+8,iso_5p:-2; Cigar 26MTC; Expression 1; Filter Pass</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">hsa-miR-320a-3p miRBase22 isomiR 42 64 . + . Read AACAGCTGGGTTGAGAGGGCGAT; UID fku54hZg1; Name hsa-miR-320a-3p; Parent hsa-mir-320a; Variant iso_snv,iso_add:+1; Cigar 2MC19MT; Expression 1; Filter Pass</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">hsa-miR-182-5p miRBase22 isomiR 23 47 . + . Read TTTGGCAATGGGAGAACTCACACTT; UID %Mo$mstsL2; Name hsa-miR-182-5p; Parent hsa-mir-182; Variant iso_snv,iso_add:+1; Cigar 11MG12MT; Expression 1; Filter Pass</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="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">hsa-miR-221-3p miRBase22 isomiR 65 86 . + . Read GGCTTAATTGTCTGCTGGGTTT; UID MQpYIu5L2; Name hsa-miR-221-3p; Parent hsa-mir-221; Variant iso_snv,iso_3p:-1; Cigar G3MTA16M; Expression 1; Filter Pass</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="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">hsa-miR-191-5p miRBase22 isomiR 16 40 . + . Read CAACGTAATCCCAAAAGCAGCTTCG; UID vSo#@kkOT2; Name hsa-miR-191-5p; Parent hsa-mir-191; Variant iso_snv,iso_add:+2; Cigar 5MT16MTCG; Expression 1; Filter Pass</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="54" style="width: 35px; color: rgba(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="LC54" class="line" lang="plaintext">hsa-let-7b-5p miRBase22 isomiR 6 30 . + . Read TGAGGTAGTAGCTTGTGTGGTTAGT; UID 7AwkRBAJL2; Name hsa-let-7b-5p; Parent hsa-let-7b; Variant iso_snvcentral_supp,iso_add:+3; Cigar 11MC10MAGT; Expression 1; Filter Pass</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="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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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">hsa-let-7d-5p miRBase22 isomiR 8 24 . + . Read TGAGGTAGTCGGTTGTA; UID 7AwGRL1; Name hsa-let-7d-5p; Parent hsa-let-7d; Variant iso_snv_central_offset,iso_3p:-5; Cigar T8MC5MTM; Expression 3; Filter Pass</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="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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">hsa-miR-140-3p miRBase22 isomiR 63 84 . + . Read ACCACAGGGTAGAACCAAGGTC; UID al$JfvAv2; Name hsa-miR-140-3p; Parent hsa-mir-140; Variant iso_snv,iso_add:+2,iso_5p:-1; Cigar 17MA2MTM; Expression 1; Filter Pass</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="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">hsa-miR-143-3p miRBase22 isomiR 61 81 . + . Read TGAGATGAAGCACTGTAGCTT; UID 7FTVqJH; Name hsa-miR-143-3p; Parent hsa-mir-143; Variant iso_snv; Cigar 20MT; Expression 35; Filter Pass</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="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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">hsa-miR-142-5p miRBase22 isomiR 14 32 . + . Read CCCATAAAGTAGAAAGCAT; UID #gcJ@VL2; Name hsa-miR-142-5p; Parent hsa-mir-142; Variant iso_snv,iso_5p:+2,iso_3p:-4; Cigar 18MT; Expression 1; Filter Pass</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="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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">hsa-miR-371a-5p miRBase22 isomiR 6 23 . + . Read TCTCAAACTGTGGGGGCA; UID 0vs3$V; Name hsa-miR-371a-5p; Parent hsa-mir-371a; Variant iso_snv_seed,iso_3p:-2; Cigar T17M; Expression 1; Filter Pass</span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">hsa-miR-1307-3p miRBase22 isomiR 80 95 . + . Read ACTCGGCGTGGCGTCG; UID sGSMYT2; Name hsa-miR-1307-3p; Parent hsa-mir-1307; Variant iso_3p:-6; Cigar 16M; Expression 4; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">hsa-let-7d-5p miRBase22 isomiR 8 33 . + . Read AGAGGTAGTCGGTTGCATAGTTTCGT; UID mAwGRnwOW1; Name hsa-let-7d-5p; Parent hsa-let-7d; Variant iso_snvcentral_supp,iso_add:+4; Cigar 9MC13MCGT; Expression 1; Filter Pass</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="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">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">hsa-miR-193b-3p miRBase22 isomiR 51 70 . + . Read AACTGGCCCTCAAAGTCCCG; UID fu#Uc9C1; Name hsa-miR-193b-3p; Parent hsa-mir-193b; Variant iso_3p:-2; Cigar 20M; Expression 1; Filter Pass</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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">hsa-miR-143-3p miRBase22 isomiR 61 81 . + . Read TGAGATGAAGCACTGTAGCTA; UID 7FTVqJr; Name hsa-miR-143-3p; Parent hsa-mir-143; Variant iso_snv; Cigar 20MA; Expression 3; Filter Pass</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">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">hsa-miR-365b-5p miRBase22 isomiR 28 47 . + . Read GAGGGACTTTCAGGGGCAGC; UID 4KHU$VV1; Name hsa-miR-365b-5p; Parent hsa-mir-365b; Variant iso_5p:+1,iso_3p:-3; Cigar 20M; Expression 2; Filter Pass</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="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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">hsa-miR-185-5p miRBase22 isomiR 15 38 . + . Read TGGAGAGAAAGGCCGTTCCTGATT; UID umThyOqp; Name hsa-miR-185-5p; Parent hsa-mir-185; Variant iso_snv,iso_add:+2; Cigar 13MC9MT; Expression 1; Filter Pass</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="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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">hsa-miR-142-5p miRBase22 isomiR 14 32 . + . Read CCCATAAAGTAGAAAGCAA; UID #gcJ@V@2; Name hsa-miR-142-5p; Parent hsa-mir-142; Variant iso_snv,iso_5p:+2,iso_3p:-4; Cigar 18MA; Expression 1; Filter Pass</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="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">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">hsa-miR-30a-5p miRBase22 isomiR 6 23 . + . Read TGTAAACATCCTCGACTG; UID B@niCq; Name hsa-miR-30a-5p; Parent hsa-mir-30a; Variant iso_3p:-4; Cigar 18M; Expression 15; Filter Pass</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="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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">hsa-miR-142-5p miRBase22 isomiR 14 32 . + . Read CCCATAAAGTAGAAAGCAC; UID #gcJ@Vv2; Name hsa-miR-142-5p; Parent hsa-mir-142; Variant iso_5p:+2,iso_3p:-4; Cigar 19M; Expression 4; Filter Pass</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="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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">hsa-miR-130a-3p miRBase22 isomiR 55 71 . + . Read CAGTGCAATGTTAAAAG; UID DIo5@m1; Name hsa-miR-130a-3p; Parent hsa-mir-130a; Variant iso_3p:-5; Cigar 17M; Expression 1; Filter Pass</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="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">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">hsa-miR-7704 miRBase22 isomiR 0 18 . + . Read CCGGCGGCGGCGGCGACTG; UID yZZZZsT2; Name hsa-miR-7704; Parent hsa-mir-7704; Variant iso_snv,iso_5p:+1,iso_3p:-1; Cigar I3MCMG10MTG; Expression 1; Filter Pass</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="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">hsa-let-7a-5p miRBase22 isomiR 6 28 . + . Read TGAGGTAGTAGGTCGTATAGTTT; UID 7AwhPzwQ1; Name hsa-let-7a-5p; Parent hsa-let-7a-1; Variant iso_snv,iso_3p:+1; Cigar 13MC9M; Expression 1; Filter Pass</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="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">hsa-miR-887-3p miRBase22 isomiR 48 68 . + . Read GTGAACGGGCGCCATCCCGAG; UID 3f$En#4; Name hsa-miR-887-3p; Parent hsa-mir-887; Variant iso_3p:-1; Cigar 21M; Expression 1; Filter Pass</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="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">hsa-miR-125b-5p miRBase22 isomiR 15 38 . + . Read TCCCTGAGACCCTAACTTGTGAAT; UID 9qm#LH3o; Name hsa-miR-125b-5p; Parent hsa-mir-125b-1; Variant iso_add:+2; Cigar 22MAT; Expression 6; Filter Pass</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="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">hsa-let-7c-5p miRBase22 isomiR 11 32 . + . Read TGAGGTAGTAGTTTGTATGGTT; UID 7AwwRzAL2; Name hsa-let-7c-5p; Parent hsa-let-7c; Variant iso_snv; Cigar 11MT10M; Expression 2; Filter Pass</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="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">hsa-miR-372-3p miRBase22 isomiR 43 66 . + . Read AAGTGCTGCGACATTTGAGCTTTC; UID cII8p76O; Name hsa-miR-372-3p; Parent hsa-mir-372; Variant iso_snv,iso_add:+2,iso_5p:-1; Cigar 20MTMTC; Expression 1; Filter Pass</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="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">hsa-miR-372-3p miRBase22 isomiR 42 65 . + . Read NAAGTGCTGCGACATTTGAGCGTT; UID .; Name hsa-miR-372-3p; Parent hsa-mir-372; Variant iso_snv,iso_add:+1; Cigar N22MT; Expression 1; Filter Pass</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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">hsa-miR-320a-3p miRBase22 isomiR 42 64 . + . Read AAAAGCTGGGTTGAGAGGGAGTT; UID @ku54h4Q1; Name hsa-miR-320a-3p; Parent hsa-mir-320a; Variant iso_snv,iso_add:+1; Cigar 19MAMTT; Expression 1; Filter Pass</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="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">hsa-miR-195-5p miRBase22 isomiR 15 38 . + . Read TAGCAGCACAGAAATATTGGTCGT; UID JDtmopAS; Name hsa-miR-195-5p; Parent hsa-mir-195; Variant iso_snv,iso_add:+3; Cigar 20MTCGT; Expression 1; Filter Pass</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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">hsa-miR-10400-5p miRBase22 isomiR 4 22 . + . Read CGGCGGCGACTCTGGACGC; UID GGCjudv2; Name hsa-miR-10400-5p; Parent hsa-mir-10400; Variant iso_snvcentral_supp,iso_add:+1,iso_5p:-3; Cigar 8MA6MA2MC; Expression 13; Filter Pass</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="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">hsa-miR-17-3p miRBase22 isomiR 51 74 . + . Read ACTGCAGTGAAGGCACTTGTAGAA; UID sV3cVHWT; Name hsa-miR-17-3p; Parent hsa-mir-17; Variant iso_add:+2; Cigar 22MAM; Expression 1; Filter Pass</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="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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">hsa-miR-181a-3p miRBase22 isomiR 63 92 . + . Read AACCATCGACCGTTGATTGTATCGTATGCC; UID fnCyRpWPzX; Name hsa-miR-181a-3p; Parent hsa-mir-181a-1; Variant iso_snv,iso_add:+7,iso_5p:+1; Cigar 21MTMG4MCM; Expression 1; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">hsa-miR-140-3p miRBase22 isomiR 62 80 . + . Read TACCACAGGGTAGAACCCC; UID NthWT#v2; Name hsa-miR-140-3p; Parent hsa-mir-140; Variant iso_snv,iso_3p:-2; Cigar 17MCM; Expression 1; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">hsa-let-7c-5p miRBase22 isomiR 14 32 . + . Read GGTAGTAGGTTGTATGGTC; UID AwhRzAv2; Name hsa-let-7c-5p; Parent hsa-let-7c; Variant iso_snv,iso_5p:-3; Cigar 18MC; Expression 1; Filter Pass</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">hsa-let-7b-5p miRBase22 isomiR 6 27 . + . Read TGAGGTAGTAGGTTGTGCGGTT; UID 7AwhRIAL2; Name hsa-let-7b-5p; Parent hsa-let-7b; Variant iso_snv; Cigar 17MC4M; Expression 35; Filter Pass</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">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">hsa-miR-181c-5p miRBase22 isomiR 27 49 . + . Read AACATTCAACCTGTCGGTGAGTT; UID fpviYA4Q1; Name hsa-miR-181c-5p; Parent hsa-mir-181c; Variant iso_3p:+1; Cigar 23M; Expression 1; Filter Pass</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="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">hsa-let-7f-5p miRBase22 isomiR 7 33 . + . Read TGAGGTAGTAGATTGTATAGTTCTTGT; UID 7AwmRzw0B; Name hsa-let-7f-5p; Parent hsa-let-7f-1; Variant iso_add:+5; Cigar 22MCMTMT; Expression 1; Filter Pass</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="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">hsa-let-7c-5p miRBase22 isomiR 11 35 . + . Read TGAGGTAGTAGGTTGTATGGTTCAT; UID 7AwhRzAUL2; Name hsa-let-7c-5p; Parent hsa-let-7c; Variant iso_add:+3; Cigar 22MCMT; Expression 1; Filter Pass</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="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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">hsa-let-7b-5p miRBase22 isomiR 6 24 . + . Read TGGGGTTGTAGGTTGTGTG; UID uABhRBT2; Name hsa-let-7b-5p; Parent hsa-let-7b; Variant iso_snv_central_offset,iso_3p:-3; Cigar 2MG3MT12M; Expression 1; Filter Pass</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="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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">hsa-let-7b-5p miRBase22 isomiR 6 28 . + . Read TGAGGTAGTAGGTTGTGTGTTTT; UID 7AwhRB5Q1; Name hsa-let-7b-5p; Parent hsa-let-7b; Variant iso_snv,iso_3p:+1; Cigar 19MT3M; Expression 2; Filter Pass</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="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">hsa-let-7i-5p miRBase22 isomiR 6 29 . + . Read TGAGGTAGTAGTTTGTGCTCGTAT; UID 7AwwRIPz; Name hsa-let-7i-5p; Parent hsa-let-7i; Variant iso_snv,iso_add:+2; Cigar 19MCGMAT; Expression 1; Filter Pass</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="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">hsa-let-7f-5p miRBase22 isomiR 7 26 . + . Read TGAGGTAGTAGATTGTATTC; UID 7AwmRzU1; Name hsa-let-7f-5p; Parent hsa-let-7f-1; Variant iso_snv,iso_3p:-2; Cigar 18MTC; Expression 6; Filter Pass</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="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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">hsa-miR-382-3p miRBase22 isomiR 47 66 . + . Read AATCATTCACGGACAACACT; UID onUGllr1; Name hsa-miR-382-3p; Parent hsa-mir-382; Variant iso_3p:-1; Cigar 20M; Expression 2; Filter Pass</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="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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">hsa-miR-221-3p miRBase22 isomiR 65 89 . + . Read AGCTACATTGTCTGCTGGGTTAATC; UID kNpYIu5ov2; Name hsa-miR-221-3p; Parent hsa-mir-221; Variant iso_snv,iso_add:+2; Cigar 21MAATC; Expression 2; Filter Pass</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="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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">hsa-miR-423-5p miRBase22 isomiR 17 37 . + . Read TGAGGGGCAGAGAGCGAGACT; UID 7$V4k4s; Name hsa-miR-423-5p; Parent hsa-mir-423; Variant iso_3p:-2; Cigar 21M; Expression 8; Filter Pass</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="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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">hsa-miR-762 miRBase22 isomiR 49 70 . + . Read GGGGCTGGGGCTGGGGCCGGTC; UID $6$6$XAv2; Name hsa-miR-762; Parent hsa-mir-762; Variant iso_snv; Cigar 11MT7MGTM; Expression 1; Filter Pass</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="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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">hsa-miR-101-3p miRBase22 isomiR 46 67 . + . Read GTCCAGTACTGTGATAACTGAA; UID YDNBFf7@2; Name hsa-miR-101-3p; Parent hsa-mir-101-1; Variant iso_snv,iso_5p:+1; Cigar 2MC19M; Expression 1; Filter Pass</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="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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">hsa-miR-449b-5p.SNPA miRBase22 isomiR 16 34 . + . Read AGGCAGTGTATCGTTAGCT; UID hDBe5kL2; Name hsa-miR-449b-5p.SNPA; Parent hsa-mir-449b; Variant iso_3p:-3; Cigar 19M; Expression 3; Filter Pass</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="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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">hsa-miR-3606-3p miRBase22 isomiR 40 57 . + . Read TTAAAATTTCTGTAACCT; UID Q@%qLi; Name hsa-miR-3606-3p; Parent hsa-mir-3606; Variant iso_snv,iso_5p:+2,iso_3p:-5; Cigar 11MGMA2MCT; Expression 1; Filter Pass</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="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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">hsa-miR-140-3p miRBase22 isomiR 62 80 . + . Read TACCACAGGGTAGAAACCC; UID NthWTav2; Name hsa-miR-140-3p; Parent hsa-mir-140; Variant iso_snv,iso_3p:-2; Cigar 15MAMCM; Expression 1; Filter Pass</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="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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">hsa-miR-199a-3p.SNPC miRBase22 isomiR 47 69 . + . Read ACAGTAGTCTGCAACTTGGTTTC; UID lWYIfR5U1; Name hsa-miR-199a-3p.SNPC; Parent hsa-mir-199a-1; Variant iso_snv,iso_add:+1; Cigar 13MAC6MTC; Expression 1; Filter Pass</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="plaintext">hsa-let-7g-5p miRBase22 isomiR 5 25 . + . Read TGAGGTAGTAGTTTGTACGGT; UID 7AwwRNA; Name hsa-let-7g-5p; Parent hsa-let-7g; Variant iso_snv,iso_3p:-1; Cigar 18MG2M; Expression 2; Filter Pass</span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">hsa-miR-320a-3p miRBase22 isomiR 42 66 . + . Read AAAAGCTGGGTTGAGATGGCGATCG; UID @ku54bZeT2; Name hsa-miR-320a-3p; Parent hsa-mir-320a; Variant iso_snv,iso_add:+3; Cigar 16MT5MTCG; Expression 1; Filter Pass</span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">hsa-miR-181b-5p miRBase22 isomiR 37 59 . + . Read ACATTCATTGCTGTCGGTGGTCG; UID lOp6YAAC1; Name hsa-miR-181b-5p; Parent hsa-mir-181b-1; Variant iso_snv,iso_add:+1,iso_5p:-1; Cigar 20MTCG; Expression 1; Filter Pass</span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">hsa-miR-34a-5p miRBase22 isomiR 22 45 . + . Read TGGCAGTGTCTTAGCTGGTTGTTC; UID uDBHkuRO; Name hsa-miR-34a-5p; Parent hsa-mir-34a; Variant iso_add:+2; Cigar 23MC; Expression 1; Filter Pass</span>
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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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">hsa-miR-145-5p miRBase22 isomiR 16 39 . + . Read GTCCAGTTTTCCCAGGAATCCCAT; UID YD%9DT9n; Name hsa-miR-145-5p; Parent hsa-mir-145; Variant iso_snv,iso_3p:+1; Cigar 22MAM; Expression 1; Filter Pass</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">hsa-miR-1301-3p miRBase22 isomiR 48 70 . + . Read TTGCAGCTGCCTGGGAGAGACTT; UID RDqi$m8Q1; Name hsa-miR-1301-3p; Parent hsa-mir-1301; Variant iso_snv,iso_3p:-1; Cigar 17MA5M; Expression 1; Filter Pass</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">hsa-miR-3917 miRBase22 isomiR 52 67 . + . Read GCTCGGACTGAGCAGG; UID 6Gs4DT2; Name hsa-miR-3917; Parent hsa-mir-3917; Variant iso_3p:-4; Cigar 16M; Expression 1; Filter Pass</span>
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">hsa-miR-99b-5p miRBase22 isomiR 7 22 . + . Read CACCCGTAGAACCGAC; UID tyJfCv2; Name hsa-miR-99b-5p; Parent hsa-mir-99b; Variant iso_3p:-6; Cigar 16M; Expression 2; Filter Pass</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">hsa-miR-372-3p miRBase22 isomiR 43 62 . + . Read AAGTGCTGCGACATTTGAGC; UID cII8p7V1; Name hsa-miR-372-3p; Parent hsa-mir-372; Variant iso_5p:-1,iso_3p:-2; Cigar 20M; Expression 105; Filter Pass</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">hsa-miR-140-3p miRBase22 isomiR 62 90 . + . Read TACCACAGGGTAGAACCACGGATAGTAAG; UID NthWTxGgWm1; Name hsa-miR-140-3p; Parent hsa-mir-140; Variant iso_add:+8; Cigar 22MT2MTMAG; Expression 1; Filter Pass</span></pre>
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<li id="a9e0c5abd611157a2d6fb457e24c28dfb68102d0">
<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#a9e0c5abd611157a2d6fb457e24c28dfb68102d0"><strong>data/examples/annotate/miRNA_sample_list.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hsa-miR-6727-5p</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">hsa-miR-409-3p</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">hsa-miR-30a-5p</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">hsa-miR-372-3p</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">hsa-miR-26a-5p</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">hsa-miR-142-5p</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">hsa-miR-365b-5p</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">hsa-miR-142-5p</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">hsa-miR-142-5p</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">hsa-miR-7704</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">hsa-miR-3606-3p</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">hsa-miR-372-3p</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">hsa-miR-372-3p</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">hsa-let-7a-5p</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">hsa-miR-92b-3p</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">hsa-miR-140-3p</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">hsa-miR-6866-5p</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">hsa-miR-3926</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">hsa-miR-576-3p</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">hsa-miR-10400-5p</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">hsa-miR-4655-5p.SNPC</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">hsa-miR-23a-3p</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">hsa-miR-140-3p</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">hsa-miR-103a-3p</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">hsa-miR-140-3p</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">hsa-miR-664a-5p.SNPC</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">hsa-miR-142-5p</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">hsa-miR-26a-5p</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">hsa-miR-10400-5p</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">hsa-miR-192-5p</span></pre>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#6dc287cbfb49fb175c2e84f9656a3af0302a6f3e"><strong>data/examples/annotate/query_sample.db</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># SQLite Command Options</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`mirtop sql`</span> package allows users to create and query a SQLite database using GFF3 file format as input. This option creates a database with two tables such as summary and data<span class="se" style="color: #d14;">\_</span>sets. The summary table contains the header portion of the gff file and data<span class="se" style="color: #d14;">\_</span>sets contains the body of the gff containing the rest of the information related to miRNAs. </span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">Use <span class="sb" style="color: #d14;">`mirtop sql -h`</span> to display help information</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">```</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">mirtop sql -h</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">SQL arguments:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">['sql', '-h']</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">usage: mirtop sql [-h] [--db] (-c | -q) [--gff] [-o] [-t] [-txto] [-col] [-n]</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"> [-miR] [-var] [-f] [-l] [-e] [-d] [-vd]</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">optional arguments:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"> -h, --help show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"> --db SQL Database name. (default: mirtop.db)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"> -c, --create Creates a SQLite database from GFF</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"> -q, --query Query from a SQLite database</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"> -d, --debug max verbosity mode</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"> -vd, --print_debug print debug messages on terminal</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">SQL create usage mode:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"> --gff GFF file with precursor and mature position to genome</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"> -o , --out Directory of output files</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">SQL query usage mode:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"> -t , --table Specify table name to use</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"> -txto , --txtout Writes the output of the query to a file speficied. Format (-fmt) is a tab-delimited text file by default</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"> -col , --columns Select specific columns from the table to display (Default: all columns), or use with -n option to return n-counts. For information of the available columns see 'show-schema' or 'show-columns'. NOTE: option -e select must be applied!</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"> -n , --count Returns 'n' counts for the query. Options 'T' for True, if not 'F' (Default: -n F). NOTE: option -e select must be applied and accepts only one column from -col option.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"> -miR , --miRNA Specify the miRNA names to query. For multiple miRNAs use comma(,) as separator; or supply a text file (.txt) separated with a new line character.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"> -pm , --miRNA_prefix (3 digit species code, ex. hsa)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"> Specify the prefix name for miRNAs to query. Example: -pm hsa -miR let-7a-5p results into querying hsa-let-7a-5p.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"> -var , --variant Specify one or more types of variants to query. Use comma(,) as separator</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"> The following choices are supported:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"> iso_5p - indicates the shift at the reference 5' miRNA</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"> iso_3p - indicates the shift at the reference 3' miRNA</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"> iso_add3p - Number of non-template nucleotides added at 3p</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"> iso_add5p - Number of non-template nucleotides added at 5p</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"> iso_snv_seed - when affected nucleotides are between [2-7]</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"> iso_snv_central_offset - when affected nucleotide is at position [8]</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"> iso_snv_central - when affected nucleotides are between [9-12]</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"> iso_snv_central_supp - when affected nucleotides are between [13-17]</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"> iso_snv - anything else</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"> -f , --filter Specify Filter tag attribute. Options: Pass, Reject. (Default: None)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"> -l , --limit Specify the number of rows to output. (Example: --limit 30, to limit the first 30 rows)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"> -e , --expr Expression is the query that you want to run; (-e "<statement>")</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"> Choices supports the following:</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"> show-tables - Displays tables in the database (default: mirtop.db)</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"> show-schema - Displays the table schema (requires -t)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"> show-columns - Displays available columns in the table</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"> describe-gff - Prints out the header information from the GFF file</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"> isomirs-per-mirna - Displays the count of isomiRs for miRNA (requires -miR)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"> select - Allows specific query construction.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"> Example: mirtop sql --db tmp_mirtop/SRR333680_revised2.db -qe select -var iso_5p,iso_3p -miR hsa-let-7a-5p,hsa-let-7d-5p -l 30</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"> The above expression evaluates to selecting miRNAs in -miR with variants in -var and prints out the first 30 rows in --limit.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Creating Database </span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`mirtop sql -c`</span> takes <span class="sb" style="color: #d14;">`--gff`</span> gff3 file and creates a database with name <span class="sb" style="color: #d14;">`--db`</span> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### From GFF3 to SQLite database</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown">git clone mirtop</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown">cd mirtop/data</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown">You can use the example data to create a database file from GFF3. </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown">mirtop sql -c --gff examples/annotate/SQL_sample.gff -o examples/annotate/ --db SQL_sample.db</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown">NOTE-1: If you are re-creating the database with the same name, make sure to delete the existing database in the working directory. As the database from the same set of samples will append the gff rows to the existing database and different set of samples throws an error as shown below.</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="sb" style="color: #d14;">`sqlite3.OperationalError: table data_sets has xy columns but yz values were supplied`</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown">Where, xy is the number of columns present in database and yz are the number of column-values sent to append to the database.</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Querying a Database</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown">Understanding the database structure helps to quickly query and fetch the results. The following content lists the useful commands to query based on the availabe options. To start with the available options type: <span class="sb" style="color: #d14;">`mirtop sql -h`</span>. </span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown">NOTE-2: To query from a database, the argument <span class="sb" style="color: #d14;">`mirtop sql -q --db <db_name.db>`</span> must always be specified with the correct name of the database along with absolute path (if required). The query will begin with an expression (-e) that is specified by the User. Passing a suitable query is mandatory such as: <span class="sb" style="color: #d14;">`mirtop sql -q --db <db_name.db> -e <expression>`</span>. The following expressions allows users the ability to query from the database:</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"><span class="p">*</span> show-tables - Displays tables in the database (default: mirtop.db)</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="p">*</span> show-schema - Displays the table schema (requires -t)</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="p">*</span> show-columns - Displays available columns in the table</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"><span class="p">*</span> describe-gff - Prints out the header information from the GFF file</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="p">*</span> isomirs-per-mirna - Displays the count of isomiRs for miRNA (requires -miR)</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="p">*</span> select - Allows specific query construction </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### show-tables:</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown">Display the contents of the database. The data or information from a gff file is loaded as a table, and the collection of tables make it a database. To see the contents of the database, we should see the available tables in the database. </span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">cd mirtop/data</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown">You can use the example data (query<span class="se" style="color: #d14;">\_</span>sample.db) to query the contents of the database. </span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e show-tables</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"><span class="p">```</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown">OUTPUT: </span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown">11/29/2019 01:03:49 INFO Run Convert GFF.</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"> +------------------------- +</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"> | Tables |</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"> +------------------------- +</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"> | data_sets |</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"> | summary |</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"> +------------------------- +</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown">11/29/2019 01:03:49 INFO It took 0.000 minutes </span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### show-schema: </span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown">Display the schema of a table. The table schema represents the data type of each column and lists available columns such as samples names. Generally this information is essential for developers and can aid in debugging any errors during the query operation. show-schema essentially requires one to specify a table name for which the schema is intended to be displayed. </span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e show-schema -t summary</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown">OUTPUT:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown">11/29/2019 01:13:55 INFO Run Convert GFF.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"> +---------------------------------------------------------+</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"> | Sl | Field | Type | NULL | Key |</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"> +---------------------------------------------------------+</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"> | 3 | tools | text | NO | |</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"> | 4 | commands_exec | text | NO | |</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"> | 5 | filter_tags | text | NO | |</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"> | 6 | citation | text | NO | |</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"> | 7 | records | real | NO | |</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"> | 8 | date_stamp | text | NO | |</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"> +---------------------------------------------------------+</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown">11/29/2019 01:13:55 INFO It took 0.000 minutes</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"><span class="p">```</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### show-columns: Query the columns of the table</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown">This is similar to show-schema, however, only columns from the table are listed excluding the data type and other information. This is required for select query options, explained later. </span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown">NOTE-3: This parameter is only available for table data<span class="se" style="color: #d14;">\_</span>sets. </span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"><span class="p">```</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e show-columns </span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown">OUTPUT:</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown">11/29/2019 01:18:55 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown">Serial Column names</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"> 1 seqID</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"> 2 source_file</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"> 3 type</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"> 4 start</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"> 5 end</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"> 6 score</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"> 7 strand</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"> 8 phase</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"> 9 UID</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"> 10 Read</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"> 11 Name</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"> 12 Parent</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"> 13 Variant</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"> 14 iso_5p</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"> 15 iso_3p</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"> 16 iso_add3p</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="markdown"> 17 iso_add5p</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="markdown"> 18 iso_snv</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"> 19 iso_snv_seed</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="markdown"> 20 iso_snv_central</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"> 21 iso_snv_central_offset</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"> 22 iso_snv_central_supp</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"> 23 source</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"> 24 cigar</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"> 25 hits</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown"> 26 alias</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown"> 27 genomic_pos</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown"> 28 filter</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"> 29 seed_fam</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="markdown"> 30 SRR333680_1</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="markdown"></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown">11/29/2019 01:18:55 INFO It took 0.000 minutes</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"><span class="p">```</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="markdown"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### describe-gff: </span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown">This option prints out the header information of the gff3 (table: summary) </span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="markdown"><span class="p">```</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e describe-gff </span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"><span class="p">```</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="markdown">OUTPUT:</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="markdown"><span class="p">```</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown">11/29/2019 01:21:18 INFO Run Convert GFF.</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="markdown">Serial Column names Description</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown"> 1 version "--"</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"> 2 source "miRBase22"</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="markdown"> 3 data_sets "SRR333680_1"</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="markdown"> 4 tools "--"</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"> 5 commands_exec "--"</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown"> 6 filter_tags "--"</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown"> 7 citation "--"</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"> 8 records "11672.0"</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown"> 9 date_stamp "November 22, 2019 16:41:50"</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown">11/29/2019 01:21:18 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### isomirs-per-mirna: </span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown">This expression provides a summary of the number of the isomiRs for the query miRNA (<span class="sb" style="color: #d14;">`-miR`</span>)</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown">Query miRNA (<span class="sb" style="color: #d14;">`-miR`</span> or <span class="sb" style="color: #d14;">`--miRNA`</span>) can be a particular miRNA of interest, or list of a few miRNAs (separated by comma) or a file of miRNAs (.txt file). The output can be redirected to a text document with <span class="sb" style="color: #d14;">`-txto <text_file.txt>`</span> argument. The users can also chooses the prefix for the miRNAs with <span class="sb" style="color: #d14;">`-pm`</span>. For example: A query <span class="sb" style="color: #d14;">`-pm hsa -miR let-7a-5p,let-7d-5p`</span> will result into querying the database as <span class="sb" style="color: #d14;">`-miR hsa-let-7a-5p,hsa-let-7d-5p`</span>. </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e isomirs-per-mirna -miR hsa-let-7a-5p</span>
</pre>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"> (-- OR --)</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e isomirs-per-mirna -miR hsa-let-7a-5p,hsa-let-7d-5p </span>
</pre>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"> (-- OR --)</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e isomirs-per-mirna -miR let-7a-5p,let-7d-5p -pm hsa </span>
</pre>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"> (-- OR --)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e isomirs-per-mirna -miR examples/annotate/miRNA_sample_list.txt -txto examples/annotate/queryOutput_isomirs.txt</span>
</pre>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown">OUTPUT:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown">11/29/2019 02:26:44 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown">OUTPUT:</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">1. isomiRs for miRNA hsa-let-7a-5p: 397</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown">2. isomiRs for miRNA hsa-let-7d-5p: 59</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown">11/29/2019 02:26:44 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### select: </span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown">This expression represents the SELECT statement used in MySQL database. It offers a lot of query options and can be combined with one or more optional arguments mentioned below. </span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown"><span class="p">*</span> limit (<span class="sb" style="color: #d14;">`-l or --limit`</span>): Specify the number of rows to output</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown">The following command uses the conventional "SELECT <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> FROM data<span class="se" style="color: #d14;">\_</span>sets" option to display the contents of the table data<span class="se" style="color: #d14;">\_</span>sets from database query<span class="se" style="color: #d14;">\_</span>sample.db. However using <span class="sb" style="color: #d14;">`-l 2 or --limit 2`</span> limits the output to display only the first two rows. If -l is not provided, it prints out all of the rows on the terminal (or) prints to a file if <span class="sb" style="color: #d14;">`-txto fileName.txt`</span> is provided. </span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="markdown"><span class="p">```</span><span class="nl"> </span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select --limit 2</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown">OUTPUT:</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="markdown">11/29/2019 03:04:28 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="markdown">seqID source_file type start end score strand phase UID Read Name Parent Variant iso_5p iso_3p iso_add3p iso_add5p iso_snv iso_snv_seed iso_snv_central iso_snv_central_offset iso_snv_central_supp source cigar hits alias genomic_pos filter seed_fam SRR333680_1</span>
</pre>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="markdown">hsa-miR-342-3p miRBase22 isomiR 61.0 85.0 . + . 0t@TeV#5v2 TCTCACAAAGAAATCGCACCCGTTC hsa-miR-342-3p hsa-mir-342 iso_snp,iso_add:+2 None None None None 1.0 0.0 0.0 0.0 0.0 miRBase22 7MA15MTC None None None Pass None 1</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="markdown">hsa-let-7i-5p miRBase22 isomiR 6.0 28.0 . + . 7AwwRIB71 TGAGGTAGTAGTTTGTGCTGTTG hsa-let-7i-5p hsa-let-7i iso_3p:+1 None 1.0 None None 0.0 0.0 0.0 0.0 0.0 miRBase22 23M None None None Pass None 1</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="markdown">11/29/2019 03:04:28 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="markdown">NOTE-4: In the above query option, we could limit the number of rows to be printed. What about columns? Can we limit them as well? and the answer is Yes. </span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="markdown"><span class="p">*</span> columns: Select specific columns from the table to display</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="markdown">The following command use the conventional "SELECT seqID,UID,Read,iso<span class="se" style="color: #d14;">\_</span>5p,iso<span class="se" style="color: #d14;">\_</span>3p,start,end FROM data<span class="se" style="color: #d14;">\_</span>sets LIMIT 2" option to display the contents of the table data<span class="se" style="color: #d14;">\_</span>sets from database query<span class="se" style="color: #d14;">\_</span>sample.db for specific columns. It prints out all the rows on the terminal (or) prints to a file if <span class="sb" style="color: #d14;">`-txto fileName.txt`</span> is provided. </span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="markdown"><span class="p">```</span><span class="nl"> </span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -l 2 -col seqID,UID,Read,iso_5p,iso_3p,start,end</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="markdown">OUTPUT:</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="markdown">11/29/2019 03:28:40 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown">seqID UID Read iso_5p iso_3p start end</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown">hsa-miR-342-3p 0t@TeV#5v2 TCTCACAAAGAAATCGCACCCGTTC None None 61.0 85.0</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="markdown">hsa-let-7i-5p 7AwwRIB71 TGAGGTAGTAGTTTGTGCTGTTG None 1.0 6.0 28.0</span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown">11/29/2019 03:28:40 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="markdown"><span class="p">```</span> </span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="markdown"><span class="p">*</span> miRNA: Specify one or more miRNA to query. </span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="markdown">The user can specify miRNAs to query from the database. Use comma (miRNA-1,NO-SPACES,miRNA-n) to separate miRNAs while passing as an argument. For large set of query miRNAs use a text-file as input, separated by new line character. If short names are preffered over including the species name every time, then please refer to argument <span class="sb" style="color: #d14;">`-pm`</span> or <span class="sb" style="color: #d14;">`--miRNA_prefix`</span> to prefix the sepcies name along with the names of miRNAs. </span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="markdown"><span class="p">```</span><span class="nl"> </span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -l 4 -col seqID,UID,Read,iso_5p,iso_3p,start,end -miR hsa-let-7i-5p</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="markdown">OUTPUT:</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="markdown">seqID UID Read iso_5p iso_3p start end</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="markdown">hsa-let-7i-5p 7AwwRIB71 TGAGGTAGTAGTTTGTGCTGTTG None 1.0 6.0 28.0</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="markdown">hsa-let-7i-5p 7AwwRIBL1 TGAGGTAGTAGTTTGTGCTGTTA None None 6.0 28.0</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="markdown">hsa-let-7i-5p 7AwwRIBU1 TGAGGTAGTAGTTTGTGCTGTTC None None 6.0 28.0</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="markdown">hsa-let-7i-5p 7AwwRIBQ1 TGAGGTAGTAGTTTGTGCTGTTT None None 6.0 28.0</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="markdown">11/29/2019 03:43:21 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="markdown"><span class="p">*</span> variant: Specify the query with one or more variant types. The following variant types can be queried using <span class="sb" style="color: #d14;">`-var`</span> argument. </span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="markdown"><span class="p"> *</span> iso_5p - indicates the shift at the reference 5' miRNA</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="markdown"><span class="p"> *</span> iso_3p - indicates the shift at the reference 3' miRNA</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="markdown"><span class="p"> *</span> iso_add3p - number of non-template nucleotides added at 3p</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="markdown"><span class="p"> *</span> iso_add5p - number of non-template nucleotides added at 5p</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="markdown"><span class="p"> *</span> iso_snv_seed - when affected nucleotides are between [2-7]</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="markdown"><span class="p"> *</span> iso_snv_central_offset - when affected nucleotide is at position [8]</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="markdown"><span class="p"> *</span> iso_snv_central - when affected nucleotides are between [9-12]</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="markdown"><span class="p"> *</span> iso_snv_central_supp - when affected nucleotides are between [13-17]</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="markdown"><span class="p"> *</span> iso_snv - anything else</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="markdown">The conventional query for selecting rows with TRUE values of iso_5p, iso_3p and iso_snv_central_offset would be as "SELECT <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> FROM data_sets WHERE iso_5p!="None" AND iso_3p!="None" AND iso_snv_central_offset!=0". In <span class="sb" style="color: #d14;">`mirtop sql`</span> we can specifiy the same as shown in the example. </span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -var iso_5p,iso_3p,iso_snv_central_offset -l 5</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="markdown">OUTPUT:</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="markdown">12/02/2019 11:52:39 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="markdown">seqID source_file type start end score strand phase UID Read Name Parent Variant iso_5p iso_3p iso_add3p iso_add5p iso_snv iso_snv_seed iso_snv_central iso_snv_central_offset iso_snv_central_supp source cigar hits alias genomic_pos filter seed_fam SRR333680_1</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="markdown">hsa-miR-6727-5p miRBase22 isomiR 8.0 26.0 . + . uMcGq6v2 TGGGGCAAGCGGCTGGCTC hsa-miR-6727-5p hsa-mir-6727 iso_snv_central_offset,iso_5p:-2,iso_3p:-2 -2.0 -2.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 T6MA8MCTC None None None Pass None 1</span>
</pre>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="markdown">hsa-miR-6809-5p miRBase22 isomiR 8.0 25.0 . + . xh@L$4 CCAAGGAAATAAGGGGAG hsa-miR-6809-5p hsa-mir-6809 iso_snv_central_offset,iso_5p:-2,iso_3p:-2 -2.0 -2.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 C8MT3MG3MG None None None Pass None 1</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(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="LC321" class="line" lang="markdown">hsa-miR-6727-5p miRBase22 isomiR 8.0 24.0 . + . hMGGDx1 AGGGGCCGGCGGCAGCC hsa-miR-6727-5p hsa-mir-6727 iso_snv_central_offset,iso_5p:-2,iso_3p:-4 -2.0 -4.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 A5MC6MAMCC None None None Pass None 1</span>
</pre>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="markdown">hsa-let-7f-5p miRBase22 isomiR 8.0 27.0 . + . . NAGGTAGTAGATTGTATAGT hsa-let-7f-5p hsa-let-7f-1 iso_snv_central_offset,iso_5p:-1,iso_3p:-1 -1.0 -1.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 N19M None None None Pass None 1</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="markdown">12/02/2019 11:52:39 INFO It took 0.001 minutes</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="markdown"><span class="p">*</span> filter: Filter attribute lets a user choose data query such that the attribute is 'Pass' for the reads from the miRNA sequencing is OK; 'Reject' if the reads are false positive; 'Reject lowcount'where the miRNA is rejected due to a low count in data. This filter decision is made by the aligner tools and is supplied to the GFF3. </span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -var iso_5p,iso_3p,iso_snv_central_offset -l 5 -f Pass</span>
</pre>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="markdown">OUTPUT:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="markdown">seqID source_file type start end score strand phase UID Read Name Parent Variant iso_5p iso_3p iso_add3p iso_add5p iso_snv iso_snv_seed iso_snv_central iso_snv_central_offset iso_snv_central_supp source cigar hits alias genomic_pos filter seed_fam SRR333680_1</span>
</pre>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="markdown">hsa-miR-6727-5p miRBase22 isomiR 8.0 26.0 . + . uMcGq6v2 TGGGGCAAGCGGCTGGCTC hsa-miR-6727-5p hsa-mir-6727 iso_snv_central_offset,iso_5p:-2,iso_3p:-2 -2.0 -2.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 T6MA8MCTC None None None Pass None 1</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="markdown">hsa-miR-6809-5p miRBase22 isomiR 8.0 25.0 . + . xh@L$4 CCAAGGAAATAAGGGGAG hsa-miR-6809-5p hsa-mir-6809 iso_snv_central_offset,iso_5p:-2,iso_3p:-2 -2.0 -2.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 C8MT3MG3MG None None None Pass None 1</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="markdown">hsa-miR-6727-5p miRBase22 isomiR 8.0 24.0 . + . hMGGDx1 AGGGGCCGGCGGCAGCC hsa-miR-6727-5p hsa-mir-6727 iso_snv_central_offset,iso_5p:-2,iso_3p:-4 -2.0 -4.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 A5MC6MAMCC None None None Pass None 1</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="markdown">hsa-let-7f-5p miRBase22 isomiR 8.0 27.0 . + . . NAGGTAGTAGATTGTATAGT hsa-let-7f-5p hsa-let-7f-1 iso_snv_central_offset,iso_5p:-1,iso_3p:-1 -1.0 -1.0 None None 0.0 0.0 0.0 1.0 0.0 miRBase22 N19M None None None Pass None 1</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="markdown">12/02/2019 12:33:28 INFO It took 0.001 minutes</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="markdown"><span class="p">*</span> count: Count is used to retrieve a summary for a custom query. Generally, <span class="sb" style="color: #d14;">`select * from data_sets`</span> or <span class="sb" style="color: #d14;">`select columns from data_sets`</span> is used to retrieve the information and a WHERE clause is optionally supplied such as <span class="sb" style="color: #d14;">`--variants \| --miRNA`</span> etc. This can be leveraged to get the count for a specific query, such that the query <span class="sb" style="color: #d14;">`select count(*) from data_sets`</span> or <span class="sb" style="color: #d14;">`select count(columns) from data_sets`</span> will be executed along with any optional WHERE clause. Argument <span class="sb" style="color: #d14;">`-n T`</span> where T is True else False (Default False).</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="markdown">For example: </span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="markdown">1) How many miRNA isoforms exists for a variant type iso_snv_central_offset and iso_5p?</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="markdown">2) How many miRNA isoforms exists for a variant type iso_5p and iso_3p?</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="markdown">3) How many miRNA isoforms exists for a variant type iso_5p and iso_3p for miRNA hsa-miR-142-5p and hsa-miR-372-3p?</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="markdown">Query in that order of example is below: </span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -var iso_5p,iso_snv_central_offset -f Pass -n T</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -var iso_5p,iso_3p -f Pass -n T</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -var iso_5p,iso_3p -f Pass -l 30 -miR hsa-miR-142-5p,hsa-miR-372-3p -n T</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="markdown">OUTPUT: </span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="markdown">Example 1: </span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="markdown">12/02/2019 01:00:03 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="markdown">COUNT(*)</span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="markdown">Unique counts for all rows is: 10</span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="markdown">12/02/2019 01:00:03 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="markdown"><span class="p">```</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="markdown">Example 2: </span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="markdown">12/02/2019 01:01:59 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="markdown">COUNT(*)</span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="markdown">Unique counts for all rows is: 751</span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="markdown">12/02/2019 01:01:59 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="markdown"><span class="p">```</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="markdown"></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="markdown">Example 3: </span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="markdown"></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="markdown"><span class="p">```</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="markdown">12/02/2019 01:02:40 INFO Run Convert GFF.</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="markdown">COUNT(*)</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="markdown">1. hsa-miR-142-5p: 28</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="markdown">2. hsa-miR-372-3p: 46</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="markdown">12/02/2019 01:02:40 INFO It took 0.000 minutes</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="markdown"><span class="p">```</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="markdown"><span class="p">*</span> txtout: Specify the query to redirect the output to a file instead of printing it on the screen. The name of the file must have an extension of (.txt). </span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="markdown">Extending from our previous example (3): How many miRNA isoforms exists for a variant type iso_5p and iso_3p for miRNA hsa-miR-142-5p and hsa-miR-372-3p and redirect the output to sample_count.txt</span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="markdown">mirtop sql -q --db examples/annotate/query_sample.db -e select -var iso_5p,iso_3p -f Pass -l 30 -miR hsa-miR-142-5p,hsa-miR-372-3p -n T -txto sample_count.txt</span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="markdown">OUTPUT:</span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="markdown">12/02/2019 01:10:06 INFO Run Convert GFF.</span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="markdown">Writing data to file: sample_count.txt</span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="markdown">12/02/2019 01:10:06 INFO It took 0.000 minutes</span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="markdown"><span class="p">```</span></span>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#6d064d69ffb7b0c563106b71f75b2cc667c1d3a3"><strong>mirtop/bam/filter.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">@@ -29,6 +29,7 @@ def tune(seq, precursor, start, cigar):</td>
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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="s" style="color: #d14;"> cigar (str): updated cigar</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="44" style="width: 35px; color: rgba(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">@@ -43,41 +44,49 @@ def tune(seq, precursor, start, cigar):</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"TUNE:: %s %s %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">mature</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;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">add</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mature</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;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"TUNE:: %s %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">add</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">subs</span><span class="p">,</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;">add</span><span class="p">),</span> <span class="n" style="color: #333;">make_cigar</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">mature</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">mature</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">error</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC57" 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;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">add</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</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;">seq</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">prob</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="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prob</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="LC60" class="line" lang="python"> <span class="n" style="color: #333;">add</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">add</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">add</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">add</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="LC69" class="line" lang="python"> <span class="n" style="color: #333;">add_position</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="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">add</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">positions_to_look</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">*</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;">seq</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)]</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">is_overlapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">([</span><span class="n" style="color: #333;">value</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">positions_to_look</span><span class="p">])</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_overlapped</span><span class="p">:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">positions_to_look</span><span class="p">:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">prob</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="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prob</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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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">add</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">])</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">]:</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">add</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">])</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">add</span><span class="p">:</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">add</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">add</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">add_position</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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76
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">add_position</span><span class="p">:</span></span>
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77
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">subs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">],</span> <span class="n" style="color: #333;">mature</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">]])</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">add</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> </span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"TUNE:: %s %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">add</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="LC89" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">subs</span><span class="p">,</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;">add</span><span class="p">),</span> <span class="n" style="color: #333;">make_cigar</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">mature</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#d04a45c446a37e2475ffe20e88836cb40ca9f4b5"><strong>mirtop/command_line.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,7 @@ from mirtop.exporter import export</td>
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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;">mirtop.gff</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">validator</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.libs</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">spikeins</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.gff</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">update</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.sql</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sql</span> </span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">mirtop.libs.logger</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mylog</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +25,7 @@ def main(**kwargs):</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'args'</span><span class="p">].</span><span class="n" style="color: #333;">print_debug</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;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mylog</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#logger.warning("This is devel-live changes")</span></span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"gff"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Run annotation"</span><span class="p">)</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">reader</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"args"</span><span class="p">])</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,4 +55,7 @@ def main(**kwargs):</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"update"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Run update tools"</span><span class="p">)</span></span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">update</span><span class="p">.</span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"args"</span><span class="p">])</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"sql"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kwargs</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Run Convert GFF."</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">sql</span><span class="p">.</span><span class="n" style="color: #333;">sql_options</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"args"</span><span class="p">])</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'It took %.3f minutes'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">((</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">60</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">@@ -17,7 +17,8 @@ def parse_cl(in_args):</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"export"</span><span class="p">:</span> <span class="n" style="color: #333;">_add_subparser_export</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"validate"</span><span class="p">:</span> <span class="n" style="color: #333;">_add_subparser_validator</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"spikein"</span><span class="p">:</span> <span class="n" style="color: #333;">_add_subparser_spikein</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"update"</span><span class="p">:</span> <span class="n" style="color: #333;">_add_subparser_update</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"update"</span><span class="p">:</span> <span class="n" style="color: #333;">_add_subparser_update</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">:</span> <span class="n" style="color: #333;">_add_subparser_sql</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"small RNA analysis"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" 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;">"--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;">"store_true"</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;">"show version."</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" style="width: 35px; color: rgba(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="196" style="width: 35px; color: rgba(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">@@ -195,3 +196,59 @@ def _add_subparser_update(subparsers):</td>
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"folder of output files"</span><span class="p">)</span></span>
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196
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_add_debug_option</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">)</span></span>
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197
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_subparser_sql</span><span class="p">(</span><span class="n" style="color: #333;">subparsers</span><span class="p">):</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" 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;">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;">"sql"</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;">"SQL create or query from GFF."</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;">RawTextHelpFormatter</span><span class="p">,</span> <span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#parser.add_argument("--gff", help="GFF file with precursor and mature position to genome.")</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" 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;">'--db'</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;">''</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'</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;">'SQL Database name. (default: mirtop.db)'</span><span class="p">)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">group</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_mutually_exclusive_group</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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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-c'</span><span class="p">,</span><span class="s" style="color: #d14;">'--create'</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;">"Creates a SQLite database from GFF"</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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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-q'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--query'</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;">"Query from a SQLite database"</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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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">group1</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;">'SQL create usage mode'</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">group1</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--gff"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GFF file with precursor and mature position to genome"</span><span class="p">)</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">group1</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--out"</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;">''</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"</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;">"tmp_mirtop"</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;">"Directory of output files"</span><span class="p">)</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">group2</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;">'SQL query usage mode'</span><span class="p">)</span> </span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--table"</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;">''</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;">"Specify table name to use"</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#group2.add_argument("-txti", "--txt-in", metavar='', help="Provide the list of miRNA's in the text file as input. NOTE: List of miRNA's should be separated by new line")</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-txto"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--txtout"</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;">''</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;">"Writes the output of the query to a file speficied. Format (-fmt) is a tab-delimited text file by default"</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#group2.add_argument("-a", "--all", metavar='', help="Selects all the columns from the table")</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-col"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--columns"</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;">''</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;">"Select specific columns from the table to display (Default: all columns), or use with -n option to return n-counts. For information of the available columns see 'show-schema' or 'show-columns'. NOTE: options -e select must be applied!."</span><span class="p">)</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">group2</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"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--count"</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;">''</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;">"Returns 'n' counts for the query. Options 'T' for True, if not 'F' (Default: -n F). NOTE: options -e select must be applied! and accepts only one column from -col option."</span> <span class="p">)</span></span>
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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">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-miR"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--miRNA"</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;">''</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;">"Specify the miRNA names to query. For multiple miRNAs use comma(,) as separator; or text file (.txt) separated with new line character"</span><span class="p">)</span></span>
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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">
222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-pm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--miRNA_prefix"</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;">''</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;">"Specify the prefix name for miRNAs to query. Example: -pm hsa -miR let-7a-5p results into querying hsa-let-7a-5p"</span><span class="p">)</span></span>
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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">
223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-var"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--variant"</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;">''</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;">"""Specify one or more types of variants to query. Use comma(,) as separator </span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"><span class="s" style="color: #d14;"> Choices supports the following:</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"><span class="s" style="color: #d14;"> iso_5p - indicates the shift at the reference 5' miRNA</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"><span class="s" style="color: #d14;"> iso_3p - indicates the shift at the reference 3' miRNA</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"><span class="s" style="color: #d14;"> iso_add3p - Number of non-template nucleotides added at 3p</span></span>
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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">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"><span class="s" style="color: #d14;"> iso_add5p - Number of non-template nucleotides added at 5p</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"><span class="s" style="color: #d14;"> iso_snv_seed - when affected nucleotides are between [2-7]</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"><span class="s" style="color: #d14;"> iso_snv_central_offset - when affected nucleotides is at position [8]</span></span>
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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">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"><span class="s" style="color: #d14;"> iso_snv_central - when affected nucleotides are between [9-12]</span></span>
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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">
232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"><span class="s" style="color: #d14;"> iso_snv_central_supp - when affected nucleotides are between [13-17]</span></span>
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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">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"><span class="s" style="color: #d14;"> iso_snv - anything else</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"><span class="s" style="color: #d14;"> """</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;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--filter"</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;">''</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;">"Specify Filter tag attribute. Options: Pass, Reject. (Default: None)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-l"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--limit"</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;">''</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;">"Specify the number of rows to output. (Example: --limit 30, to limit the first 30 rows)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># group2.add_argument("-imiR", "--isomiR", metavar='', help="Specify the miRNA name to query")</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># group2.add_argument("-s", "--schema", metavar='', help="Show the schema of the select tables; (-s <table_name>)")</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">group2</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--expr"</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;">''</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"""Expression is the query that you want to run; (-e </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"><statement></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;"> Choices supports the following: </span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> show-tables - Displays tables in the database (default: mirtop.db) </span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;"> show-schema - Displays the table schema (requires -t)</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"><span class="s" style="color: #d14;"> show-columns - Displays available columns in the table</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"><span class="s" style="color: #d14;"> describe-gff - Prints out the header information from the GFF file</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;"> isomirs-per-mirna - Displays the count of isomiRs for miRNA (requires -miR)</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;"> select - Allows specific query construction. </span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"><span class="s" style="color: #d14;"> Example: mirtop sql --db tmp_mirtop/SRR333680_revised2.db -qe select -var iso_5p,iso_3p -miR hsa-let-7a-5p,hsa-let-7d-5p -l 30</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"><span class="s" style="color: #d14;"> The above expression evaluates to selecting miRNAs in -miR with variants in -var and prints out first 30 rows in --limit </span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC252" 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;">_add_debug_option</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#27410ad28c824687ba85a7f875c5934e7cac0aea"><strong>mirtop/sql/__init__.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;">from</span> <span class="nn" style="color: #555;">mirtop.libs</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">config</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="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">version</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># import os</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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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;">sqlite3</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">op</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># dd/mm/YY H:M:S</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">d2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">now</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%B %d, %Y %H:%M:%S"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_table</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">sample_names</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;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">cursor</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;">data_columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'seqID text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'source_file text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'type text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'start real'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">'end real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'score text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'strand text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'phase text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'UID text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Read text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Name text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Parent text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Variant text'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">'iso_5p real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_3p real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_add3p real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_add5p real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_snv real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_snv_seed real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_snv_central real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_snv_central_offset real'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'iso_snv_central_supp real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'source text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cigar text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hits real'</span><span class="p">,</span> <span class="s" style="color: #d14;">'alias text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'genomic_pos text'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filter text'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'seed_fam text'</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;">complete_headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data_columns</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sample_names</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CREATE TABLE IF NOT EXISTS data_sets(%s)"</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;">complete_headers</span><span class="p">)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">commit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">gff_insert_values</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">complete_list</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'INSERT INTO data_sets VALUES('</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="s" style="color: #d14;">"?"</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">complete_list</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">')'</span><span class="p">,</span> <span class="n" style="color: #333;">complete_list</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">commit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">sqlite3</span><span class="p">.</span><span class="n" style="color: #333;">OperationalError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"sqlite3.OperationalError: {0}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Help: Make sure to delete any existing database with tables of different schema"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print("date and time =", d2)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">insert_sql</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="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">db</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;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">db</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">conn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqlite3</span><span class="p">.</span><span class="n" style="color: #333;">connect</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC46" 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="LC47" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"mirtop.db"</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;">conn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqlite3</span><span class="p">.</span><span class="n" style="color: #333;">connect</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</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;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tools</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">commands_exec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_tags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">citation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">num_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">text</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># HEADER INFORMATION</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^## .* VERSION"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># (R)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">text</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 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="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^## source-ontology"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># (R)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">text</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 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="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^## COLDATA"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># (R)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">data_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">text</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 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;"># Might contain more than one data set</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">sample_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data_sets</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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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">sample_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'_'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sample_names</span><span class="p">]</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">string_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"text"</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">output_sample_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"{} {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">string_text</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sample_names</span><span class="p">]</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">create_table</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">output_sample_names</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^## TOOLS"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># (R)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">tools</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">text</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 class="o" style="font-weight: 600;">-</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="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">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^## CMD"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># (O)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">commands_exec</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">text</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 class="o" style="font-weight: 600;">-</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="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^## FILTER"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># (O)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">filter_tags</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">text</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 class="o" style="font-weight: 600;">-</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="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^## REFERENCE"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># (O)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">citation</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">text</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 class="o" style="font-weight: 600;">-</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="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># BODY - INFORMATION</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"^#"</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'='</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">lines_info_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">,</span> <span class="s" style="color: #d14;">" "</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">lines_info_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines_info_array</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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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">info_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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87
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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;">elements</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">:</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">elements</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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">([(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">)])</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'Variant'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">":"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">value_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</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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92
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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;">iso_vars</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value_list</span><span class="p">:</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">":"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iso_vars</span><span class="p">:</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">sub_k</span><span class="p">,</span> <span class="n" style="color: #333;">sub_v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iso_vars</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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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">([(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">sub_k</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">sub_v</span><span class="p">))])</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### Exception for miRge format START </span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"iso_snp"</span><span class="p">:</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"iso_snv"</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"iso_add"</span><span class="p">:</span> </span>
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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="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"iso_add3p"</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### Exception for miRge format END</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'iso_snv'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'iso_snv'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'iso_snv_seed'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'iso_snv_seed'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'iso_snv_central'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'iso_snv_central'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'iso_snv_central_offset'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'iso_snv_central_offset'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'iso_snv_central_supp'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iso_vars</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'iso_snv_central_supp'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> </span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">prefix_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'UID'</span><span class="p">),</span> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'Read'</span><span class="p">),</span> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'Name'</span><span class="p">),</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'Parent'</span><span class="p">),</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'Variant'</span><span class="p">),</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_5p'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_3p'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)),</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_add3p'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_add5p'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)),</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_snv'</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">)),</span> </span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_snv_seed'</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">)),</span> </span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_snv_central'</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">)),</span> </span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_snv_central_offset'</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">)),</span> </span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'iso_snv_central_supp'</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">)),</span> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">source</span><span class="p">,</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'Cigar'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">),</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'Hits'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">),</span> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'Alias'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">),</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'Genomic'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">),</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'Filter'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">),</span> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">'Seed_fam'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)]</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">expression_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'Expression'</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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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">complete_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix_list</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">expression_list</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">gff_insert_values</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">complete_list</span><span class="p">)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">'''CREATE TABLE IF NOT EXISTS summary(version text, source text, data_sets text, tools text,</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"><span class="s" style="color: #d14;"> commands_exec text, filter_tags text, citation text, records real, date_stamp text)'''</span><span class="p">)</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">"INSERT INTO summary(version, source, data_sets, tools, commands_exec, filter_tags, citation, "</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">"records, date_stamp) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">data_sets</span><span class="p">,</span> <span class="n" style="color: #333;">tools</span><span class="p">,</span> <span class="n" style="color: #333;">commands_exec</span><span class="p">,</span> <span class="n" style="color: #333;">filter_tags</span><span class="p">,</span> <span class="n" style="color: #333;">citation</span><span class="p">,</span> <span class="n" style="color: #333;">cnt</span><span class="p">,</span> <span class="n" style="color: #333;">d2</span><span class="p">))</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># info_dict.setdefault('Sex', None)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">commit</span><span class="p">()</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">query_sql</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("Function query is being implemented, will be updated soon!!!")</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(args)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">db</span><span class="p">:</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">db</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">conn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqlite3</span><span class="p">.</span><span class="n" style="color: #333;">connect</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"mirtop.db"</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">conn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqlite3</span><span class="p">.</span><span class="n" style="color: #333;">connect</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#c.execute("SELECT name FROM sqlite_master WHERE type = 'table';")</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#record = c.fetchall()</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(args.db)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"show-tables"</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">show_tables</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"show-schema"</span><span class="p">:</span></span>
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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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">table</span><span class="p">:</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">show_schema</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">table</span><span class="p">)</span></span>
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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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Require table name"</span><span class="p">)</span></span>
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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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: mirtop sql --query --db <input_database> -e show-schema -t <table_name>"</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"show-columns"</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">show_columns</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"describe-gff"</span><span class="p">:</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">describe_gff_info</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<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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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"isomirs-per-mirna"</span><span class="p">:</span></span>
</pre>
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<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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA</span><span class="p">:</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">stats_isomiR_per_miRNA</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" 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="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="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Require miRNA name"</span><span class="p">)</span></span>
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<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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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: mirtop sql --query --db <input_database> -e isomirs-per-mirna -miR <miRNA>"</span><span class="p">)</span></span>
</pre>
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<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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<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;">args</span><span class="p">.</span><span class="n" style="color: #333;">expr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"select"</span><span class="p">:</span></span>
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<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="n" style="color: #333;">select_query</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<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="k" style="font-weight: 600;">pass</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"></span>
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179
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">show_tables</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">):</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" +"</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" +"</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' | Tables |'</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" +"</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" +"</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">tableName</span><span class="p">,)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"><span class="s" style="color: #d14;"> select NAME from SQLITE_MASTER where TYPE='table' order by NAME;</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="p">):</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">tn_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">tableName</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">req_format_space</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tn_name</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" | {tn}{format_space}|"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">tn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tableName</span><span class="p">,</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">format_space</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">req_format_space</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">" "</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># Table name (for each table)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" +"</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" +"</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">show_schema</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">,</span> <span class="n" style="color: #333;">table_name</span><span class="p">):</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">tableName</span><span class="p">,)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;"> select NAME from SQLITE_MASTER where TYPE='table' order by NAME;</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="p">):</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print("{}:".format(tableName)) # Table name (for each table)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tableName</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">table_name</span><span class="p">:</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" +"</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">57</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"+"</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' | Sl | Field | Type | NULL | Key |'</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" +"</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">57</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"+"</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">columnID</span><span class="p">,</span> <span class="n" style="color: #333;">columnName</span><span class="p">,</span> <span class="n" style="color: #333;">columnType</span><span class="p">,</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">columnNotNull</span><span class="p">,</span> <span class="n" style="color: #333;">columnDefault</span><span class="p">,</span> <span class="n" style="color: #333;">columnPK</span><span class="p">,</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="s" style="color: #d14;">"pragma table_info('{}');"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">tableName</span><span class="p">)):</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">name_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">columnName</span><span class="p">)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">columnID_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">columnID</span><span class="p">))</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">required_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">30</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">name_size</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">req_col_size</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;">columnID_size</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" | {colSpace}{id} | {name}{space}| {type} | {null} | {pk} |"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">colSpace</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">req_col_size</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="LC220" 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;">columnID</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC221" 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;">columnName</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">space</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required_len</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="LC223" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columnType</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">columnType</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">null</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" not null"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">columnNotNull</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" NO "</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" [{}]"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">columnDefault</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">columnDefault</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"NULL"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">pk</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" *{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">columnPK</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">columnPK</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" "</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" +"</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">57</span> <span class="o" style="font-weight: 600;">*</span> <span class="s" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"+"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">show_columns</span><span class="p">(</span><span class="n" style="color: #333;">connection</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="LC232" class="line" lang="python"> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">query</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SELECT * FROM data_sets LIMIT 2"</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="n" style="color: #333;">query</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;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">fetchall</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">col_name_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">tuple</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="nb" style="color: #0086b3;">tuple</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">sl_no</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="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Serial</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Column names"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">col_name_list</span><span class="p">:</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">sl_no</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">sl_no</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="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">describe_gff_info</span><span class="p">(</span><span class="n" style="color: #333;">connection</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="LC246" class="line" lang="python"> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">query</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SELECT * FROM summary"</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">fetchone</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">col_name_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">tuple</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="nb" style="color: #0086b3;">tuple</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">sl_no</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="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Serial</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Column names</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Description"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">col_name_list</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">desc_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">desc_g</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="LC256" class="line" lang="python"> <span class="n" style="color: #333;">desc_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--"</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">sl_no</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\"</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">desc_g</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">sl_no</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">stats_isomiR_per_miRNA</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">,</span> <span class="n" style="color: #333;">miRNA_name</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="LC263" class="line" lang="python"> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">miR_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_mirnas</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="LC265" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#cur.execute('SELECT * FROM data_sets WHERE seqID=?', (miRNA_name,))</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">query</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SELECT COUNT(*) FROM data_sets WHERE seqID=? AND type='isomiR' "</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_filter</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">stat_counts</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"The results are being fetched and formated to be written to "</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;">txtout</span><span class="p">)</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#format_results()</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#with open(args.txtout, 'w') as w_stat:</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">w_stat</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">w_stat</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Serial number</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">miRNA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">isomiR Count</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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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"OUTPUT:"</span><span class="p">)</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> </span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">miRs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">miR_array</span><span class="p">:</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">miRs</span><span class="p">,</span> <span class="p">)</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#cur.execute("SELECT COUNT(*) FROM data_sets WHERE seqID=? AND type='isomiR'", t)</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">fetchall</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span><span class="p">:</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">stat_counts</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">w_stat</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">stat_counts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">miRs</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">stat_counts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">". "</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"isomiRs for miRNA "</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">miRs</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": "</span><span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">))</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">w_stat</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">WHERE_CLAUSE</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"WHERE"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">query</span><span class="p">:</span> </span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" AND "</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" WHERE "</span> </span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ALWAYS EXECUTE THIS LIMIT FUNCTION AT THE END </span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_limit</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">limit</span><span class="p">:</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" LIMIT "</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;">limit</span> </span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">query</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">query</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_filter</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">:</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WHERE_CLAUSE</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" filter='"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"' "</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">query</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" 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="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">query</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_variants</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">my_var_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'iso_5p'</span><span class="p">:</span> <span class="s" style="color: #d14;">'iso_5p != "None"'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_3p'</span><span class="p">:</span> <span class="s" style="color: #d14;">'iso_3p != "None"'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_add3p'</span><span class="p">:</span> <span class="s" style="color: #d14;">'iso_add3p != "None"'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_add5p'</span><span class="p">:</span> <span class="s" style="color: #d14;">'iso_add5p != "None"'</span><span class="p">,</span> </span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="s" style="color: #d14;">'iso_snv_seed'</span><span class="p">:</span><span class="s" style="color: #d14;">'iso_snv_seed != 0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_snv_central_offset'</span><span class="p">:</span><span class="s" style="color: #d14;">'iso_snv_central_offset != 0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_snv_central'</span><span class="p">:</span><span class="s" style="color: #d14;">'iso_snv_central != 0'</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="s" style="color: #d14;">'iso_snv_central_supp'</span><span class="p">:</span><span class="s" style="color: #d14;">'iso_snv_central_supp != 0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'iso_snv'</span><span class="p">:</span><span class="s" style="color: #d14;">'iso_snv != 0'</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">user_req_var</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;">variant</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="LC329" class="line" lang="python"> <span class="n" style="color: #333;">values_req_var</span> <span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">eachVar</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">user_req_var</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC331" 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="LC332" class="line" lang="python"> <span class="n" style="color: #333;">values_req_var</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">my_var_dict</span><span class="p">[</span><span class="n" style="color: #333;">eachVar</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">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="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Error: </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">eachVar</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> does not exist in the choices supported by (-var , --variant)</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="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"use: mirtop sql -qh for more options"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(values_req_var)</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">insert_betwn</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" AND "</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">query_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">insert_betwn</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="n" style="color: #333;">values_req_var</span> <span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WHERE_CLAUSE</span><span class="p">(</span><span class="n" style="color: #333;">query</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="LC341" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query_suffix</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">query</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;">#if args.filter:</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#query = query + " AND " + query_suffix </span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#return query</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#else:</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#query = query + "WHERE " + query_suffix </span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#return query</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_mirnas</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.txt'</span><span class="p">):</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("I am called and I am safe here to read from a file")</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">miList</span><span class="p">:</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">miR_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">miList</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">splitlines</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA_prefix</span><span class="p">:</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">element</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"-"</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">miR_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">element</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">miR_array</span><span class="p">]</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">miR_array</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC359" 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="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">miR_array</span><span class="p">)</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" 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="LC362" class="line" lang="python"> <span class="n" style="color: #333;">miR_array</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;">miRNA</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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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA_prefix</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">element</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"-"</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">miR_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">element</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">miR_array</span><span class="p">]</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">miR_array</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC367" 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="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">miR_array</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">perform_execution</span><span class="p">(</span><span class="n" style="color: #333;">conn</span><span class="p">,</span> <span class="n" style="color: #333;">query</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="LC372" class="line" lang="python"> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conn</span><span class="p">.</span><span class="n" style="color: #333;">cursor</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("QUERY: \n"+ query + "\n")</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">fetchall</span><span class="p">()</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">col_name_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">tuple</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="nb" style="color: #0086b3;">tuple</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">]</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA</span><span class="p">:</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">col_name_list</span><span class="p">,</span> <span class="n" style="color: #333;">rows</span><span class="p">)</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">format_results</span><span class="p">(</span><span class="n" style="color: #333;">col_name_list</span><span class="p">,</span> <span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format_results</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header</span><span class="p">)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">outList</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Writing data to file: "</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;">txtout</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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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">outList</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="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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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">write_to_file</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">outList</span><span class="p">)</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">:</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Unique counts for "</span><span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" is: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Unique counts for all rows is: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">eachrow</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">row_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">items</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">items</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">eachrow</span><span class="p">)</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">row_tab</span><span class="p">)</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_to_file</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">fileHandler</span><span class="p">):</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA</span><span class="p">:</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">fileHandler</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">output</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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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">:</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">fileHandler</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Unique counts for "</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;">columns</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" is:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">))</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" 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="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">eachrow</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">row_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">items</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">items</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">eachrow</span><span class="p">)</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">fileHandler</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">row_tab</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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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">select_query</span><span class="p">(</span><span class="n" style="color: #333;">connection</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="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">:</span> </span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"T"</span><span class="p">:</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SELECT COUNT("</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;">columns</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") FROM data_sets "</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" 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="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: -n is incorrect!. </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Please use -n T and optionally specify any one column in -col.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">For more options see mirtop sql -h"</span><span class="p">)</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" 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="LC424" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SELECT "</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;">columns</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" FROM data_sets "</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">:</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SELECT COUNT(*) FROM data_sets "</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SELECT * FROM data_sets "</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_filter</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">variant</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_variants</span><span class="p">(</span><span class="n" style="color: #333;">query</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="LC432" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">miRNA</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">miR_array</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_mirnas</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="LC434" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WHERE_CLAUSE</span><span class="p">(</span><span class="n" style="color: #333;">query</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="LC435" class="line" lang="python"> <span class="n" style="color: #333;">query_series</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"seqID= "</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">header_var</span><span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">outList</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Writing data to file: "</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;">txtout</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="LC441" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">miRs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">miR_array</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query_series</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">miRs</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> "</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_limit</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">rows</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perform_execution</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">,</span> <span class="n" style="color: #333;">query</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="LC446" class="line" lang="python"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">):</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header_var</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="LC450" class="line" lang="python"> <span class="n" style="color: #333;">header_var</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header</span><span class="p">)</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">outList</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">header_var</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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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">header_var</span><span class="p">)</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">row_tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">items</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">items</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">:</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">newOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">". "</span><span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">miRs</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row_tab</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">write_to_file</span><span class="p">(</span><span class="n" style="color: #333;">newOut</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">outList</span><span class="p">)</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">newOut</span><span class="p">)</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">txtout</span><span class="p">:</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"> <span class="n" style="color: #333;">write_to_file</span><span class="p">(</span><span class="n" style="color: #333;">row_tab</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">outList</span><span class="p">)</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">row_tab</span><span class="p">)</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_limit</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">perform_execution</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">,</span> <span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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470
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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>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sql_options</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="LC473" class="line" lang="python"> <span class="n" style="color: #333;">user_options</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">vars</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="LC474" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">create</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;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">insert_sql</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="LC477" 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="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: mirtop sql --create --gff <input.gff> --db <new_db_name> \(Default: mirtop.db\)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">query</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">expr</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print("Usage: mirtop sql --query --db <input_database> -e <user_query>")</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">query_sql</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="LC483" 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="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: mirtop sql --query --db <input_database> -e <user_query>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC485" 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="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: mirtop sql -h"</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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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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4
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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;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">find_packages</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" 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;">'0.4.2<span class="idiff left right">3</span>'</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" 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;">'0.4.2<span class="idiff left right">4</span>'</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'http://github.com/mirtop/mirtop'</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#d0647faf8b4f761b838cd192919a47664375a4cd"><strong>test/test_automated_analysis.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">@@ -475,4 +475,311 @@ class AutomatedAnalysisTest(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/gff/correct_file.gff"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC482" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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="LC483" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_create_1_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to incorporate GFF to SQLite</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="s" style="color: #d14;">"--gff"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/SQL_sample.gff"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="s" style="color: #d14;">"SQL_sample.db"</span><span class="p">]</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC503" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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="LC504" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC505" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_create_2_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to incorporate GFF to SQLite</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="s" style="color: #d14;">"--gff"</span><span class="p">,</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/SQL_sample.gff"</span><span class="p">,</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC521" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC523" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_showTables_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from a database to show tables using SQLite</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"> <span class="s" style="color: #d14;">"show-tables"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</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;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC539" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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="LC540" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_showSchema_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from a database to show schema using SQLite</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="s" style="color: #d14;">"show-schema"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"> <span class="s" style="color: #d14;">"-t"</span><span class="p">,</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"> <span class="s" style="color: #d14;">"summary"</span><span class="p">]</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> </span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC561" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_showColumns_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from a database to show columns using SQLite</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="s" style="color: #d14;">"show-columns"</span><span class="p">]</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_descSummary_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from a database to display the header of the GFF using SQLite</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"> <span class="s" style="color: #d14;">"describe-gff"</span><span class="p">]</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC595" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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="LC596" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC597" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_statIsomirs_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from a database to summarize isomirs per miRNA </span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="s" style="color: #d14;">"isomirs-per-mirna"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="s" style="color: #d14;">"-miR"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="s" style="color: #d14;">"hsa-let-7a-5p,hsa-let-7d-5p"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></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="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC615" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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="LC616" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC617" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_statIsomirsFile_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from a database to summarize isomirs per miRNA reading from afile</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"> <span class="s" style="color: #d14;">"isomirs-per-mirna"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="s" style="color: #d14;">"-miR"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/miRNA_sample_list.txt"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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="LC631" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC635" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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="LC636" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC637" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_SelectLimit_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from database using limit option</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python"> <span class="s" style="color: #d14;">"select"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"> <span class="s" style="color: #d14;">"--limit"</span><span class="p">,</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python"> <span class="s" style="color: #d14;">"2"</span><span class="p">]</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC655" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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="LC656" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC657" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_SelectColumns_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from database using limit option</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"> <span class="s" style="color: #d14;">"select"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"> <span class="s" style="color: #d14;">"-l"</span><span class="p">,</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"> <span class="s" style="color: #d14;">"2"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python"> <span class="s" style="color: #d14;">"-col"</span><span class="p">,</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python"> <span class="s" style="color: #d14;">"seqID,UID,Read,iso_5p,iso_3p,start,end"</span><span class="p">]</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC677" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_SelectMirna_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from database for specific miRNAs </span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"> <span class="s" style="color: #d14;">"select"</span><span class="p">,</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python"> <span class="s" style="color: #d14;">"-l"</span><span class="p">,</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python"> <span class="s" style="color: #d14;">"4"</span><span class="p">,</span> </span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python"> <span class="s" style="color: #d14;">"-col"</span><span class="p">,</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="s" style="color: #d14;">"seqID,UID,Read,iso_5p,iso_3p,start,end"</span><span class="p">,</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python"> <span class="s" style="color: #d14;">"-miR"</span><span class="p">,</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python"> <span class="s" style="color: #d14;">"hsa-let-7i-5p"</span><span class="p">]</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python"> </span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_SelectiVariant_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from database for specific variant types </span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="python"> <span class="s" style="color: #d14;">"select"</span><span class="p">,</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python"> <span class="s" style="color: #d14;">"-l"</span><span class="p">,</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="python"> <span class="s" style="color: #d14;">"5"</span><span class="p">,</span> </span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="python"> <span class="s" style="color: #d14;">"-var"</span><span class="p">,</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python"> <span class="s" style="color: #d14;">"iso_5p,iso_3p,iso_snv_central_offset"</span><span class="p">]</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> </span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_SelectFilter_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from database using filters </span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"> <span class="s" style="color: #d14;">"select"</span><span class="p">,</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="python"> <span class="s" style="color: #d14;">"-l"</span><span class="p">,</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="python"> <span class="s" style="color: #d14;">"5"</span><span class="p">,</span> </span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"> <span class="s" style="color: #d14;">"-var"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="python"> <span class="s" style="color: #d14;">"iso_5p,iso_3p,iso_snv_central_offset"</span><span class="p">,</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="python"> <span class="s" style="color: #d14;">"-f"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python"> <span class="s" style="color: #d14;">"Pass"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC747" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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="LC749" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_SelectCount_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from database to fetch counts of the return values </span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"select"</span><span class="p">,</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python"> <span class="s" style="color: #d14;">"-var"</span><span class="p">,</span> <span class="s" style="color: #d14;">"iso_5p,iso_3p"</span><span class="p">,</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="python"> <span class="s" style="color: #d14;">"-miR"</span><span class="p">,</span> <span class="s" style="color: #d14;">"hsa-miR-142-5p,hsa-miR-372-3p"</span><span class="p">,</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="python"> <span class="s" style="color: #d14;">"-n"</span><span class="p">,</span><span class="s" style="color: #d14;">"T"</span><span class="p">]</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">complete</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="LC767" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd_validate</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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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql_query_SelectTextOut_cmd</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run sql command to query from database and return the output to a text file </span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">make_workdir</span><span class="p">():</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python"> <span class="n" style="color: #333;">clcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mirtop"</span><span class="p">,</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="python"> <span class="s" style="color: #d14;">"sql"</span><span class="p">,</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python"> <span class="s" style="color: #d14;">"--db"</span><span class="p">,</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python"> <span class="s" style="color: #d14;">"../../data/examples/annotate/query_sample.db"</span><span class="p">,</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python"> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"select"</span><span class="p">,</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="python"> <span class="s" style="color: #d14;">"-var"</span><span class="p">,</span> <span class="s" style="color: #d14;">"iso_5p,iso_3p"</span><span class="p">,</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="python"> <span class="s" style="color: #d14;">"-miR"</span><span class="p">,</span> <span class="s" style="color: #d14;">"hsa-miR-142-5p,hsa-miR-372-3p"</span><span class="p">,</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python"> <span class="s" style="color: #d14;">"-n"</span><span class="p">,</span><span class="s" style="color: #d14;">"T"</span><span class="p">,</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python"> <span class="s" style="color: #d14;">"-txto"</span><span class="p">,</span><span class="s" style="color: #d14;">"sample_count.txt"</span><span class="p">]</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</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;">clcode</span><span class="p">))</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">clcode</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mirtop/-/commit/7cde033d25322c7fc507baa7abfa048ffb0438b1#0bf568057b7d974795fdf77eef231e1fe43a58b4"><strong>test/test_functions.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="308" style="width: 35px; color: rgba(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="308" style="width: 35px; color: rgba(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">@@ -308,10 +308,12 @@ class FunctionsTest(unittest.TestCase):</td>
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308
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308
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<pre style="margin: 0;"> <span id="LC308" 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;">res</span><span class="p">:</span></span>
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309
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">10</span><span class="p">:</span></span>
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310
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Wrong alignment for test 7 %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"></span>
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align_from_variants</span><span class="p">(</span><span class="s" style="color: #d14;">"AGGTAGTAGGATGTATAGAA"</span><span class="p">,</span> <span class="n" style="color: #333;">mature</span><span class="p">,</span></span>
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="s" style="color: #d14;">"iso_5p:+2,iso_3p:-2,iso_add3p:2"</span><span class="p">)</span></span>
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313
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>
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314
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Wrong alignment for test 8 %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">res</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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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"></span>
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">alignment</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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317
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_alignment</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="528" style="width: 35px; color: rgba(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">@@ -528,3 +530,35 @@ class FunctionsTest(unittest.TestCase):</td>
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528
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.gff.update</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">update_file</span></span>
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529
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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530
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="n" style="color: #333;">update_file</span><span class="p">(</span><span class="s" style="color: #d14;">"data/examples/versions/version1.0.gff"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">sql</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="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sql</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="s" style="color: #d14;">"""testing mirtop_sql in sql.py function"""</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.libs</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.sql</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sql</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" 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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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">initialize_logger</span><span class="p">(</span><span class="s" style="color: #d14;">"test SQLite Create"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC542" 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;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">Namespace</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">create</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"True"</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"SQL_sample.db"</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'data/examples/annotate/SQL_sample.gff'</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'data/examples/annotate/'</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="n" style="color: #333;">sql</span><span class="p">.</span><span class="n" style="color: #333;">sql_options</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"SQL_sample.db"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">issue64</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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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue64</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.bam.filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tune</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">add</span><span class="p">,</span> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tune</span><span class="p">(</span><span class="s" style="color: #d14;">"TATCACAGTGGCTGTTCTTTTTT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCCCCTATCACAGTGGCTGTTCTTTTTT"</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">add</span><span class="p">:</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Bad annotation in for seqs with 6T/As at the end"</span><span class="p">)</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">attr</span><span class="p">(</span><span class="n" style="color: #333;">error69</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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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_error69</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mirtop.bam.filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tune</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tune</span><span class="p">(</span><span class="s" style="color: #d14;">"CTTATCAGATTGTATTGTAATT"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"> <span class="s" style="color: #d14;">"TACATCGGCCATTATAATACAACCTGATAAGTGTTATAGCACTTATCAGATTGTATTGTAATTGTCTGTGTANNNNNNNNNNNN"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="mi" style="color: #099;">41</span><span class="p">,</span> <span class="p">[(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">22</span><span class="p">)])</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</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;">"22M"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Issue 69 is back. Variantion not detected correctly."</span><span class="p">)</span></span></pre>
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