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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-bx">Debian Med / python-bx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5">079d1e35</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-02-24T21:45:54+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.9</pre>
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<h4>11 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#87c1820b3e9b05cd007ea95036b5904546475c20">
lib/bx/__init__.py
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<li class="file-stats">
<a href="#29cdd67e006ffe226cbd820486dcf212f376602c">
lib/bx/intervals/operations/quicksect.py
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<li class="file-stats">
<a href="#1537b40f7ffdbbdf2ae5661444f7388a70ede926">
lib/bx/misc/cdb.py
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<li class="file-stats">
<a href="#afc52934ef927f0b735fed3d6f32f32ede6ea92a">
lib/bx/seq/twobit.py
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<li class="file-stats">
<a href="#9e6f610975de2315250d797c93c2336a48af5a4c">
scripts/aggregate_scores_in_intervals.py
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<li class="file-stats">
<a href="#5e13d51c89eaefc1a2d15f107f6bf87fb9dc02f8">
scripts/axt_to_lav.py
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<li class="file-stats">
<a href="#5c685d7860deb9bda05a65dc542b740d20af6718">
scripts/axt_to_maf.py
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<li class="file-stats">
<a href="#dcd8d2010a291b730a1e0a4b6421ea914ae0ec08">
scripts/bed_coverage.py
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<li class="file-stats">
<a href="#e17ff8eee288b12833a6a7764b2ae48e0794eebf">
scripts/bed_merge_overlapping.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,9 +68,9 @@ addons:</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">liblzo2-dev</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON -m pip install Cython nose numpy python-lzo<span class="idiff left right"> six</span></span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON -m pip install Cython nose numpy python-lzo</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON setup.py build_ext --inplace</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON <span class="idiff left right">setup.py</span> install</span></span>
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<td class="old_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">
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$PYTHON <span class="idiff left">-m pip</span> install<span class="idiff right"> .</span></span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC75" 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="LC76" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nosetests</span></span></pre>
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<li id="87c1820b3e9b05cd007ea95036b5904546475c20">
<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#87c1820b3e9b05cd007ea95036b5904546475c20"><strong>lib/bx/__init__.py</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.8.<span class="idiff left right">8</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.8.<span class="idiff left right">9</span>'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#29cdd67e006ffe226cbd820486dcf212f376602c"><strong>lib/bx/intervals/operations/quicksect.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,12 @@ from __future__ import print_function</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">random</span></span>
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<pre style="margin: 0;">-<span id="LC9" 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="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">time</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">process_time</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For compatibility with Python < 3.3</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;">time</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">clock</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">process_time</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">IntervalTree</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,7 +135,7 @@ class IntervalNode(object):</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">test</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">intlist</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left right">x</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">20000</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">20000</span><span class="p">):</span></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;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1000000</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 class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test</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">@@ -138,19 +143,19 @@ def main():</td>
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138
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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139
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">test</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalNode</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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140
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">intlist</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">starttime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">time</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clock</span></span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">starttime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">process_time</span></span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">5000</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC148" 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;">random</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</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="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</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;">result</span> <span class="o" style="font-weight: 600;">=</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;">test</span><span class="p">.</span><span class="n" style="color: #333;">intersect</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">linenum</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%f for tree method"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">time</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clock</span></span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">starttime</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">starttime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">time</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clock</span></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;">for</span> <span class="n" style="color: #333;"><span class="idiff left right">x</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">5000</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="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%f for tree method"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">process_time</span></span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">starttime</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">starttime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">process_time</span></span><span class="p">()</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">5000</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC155" 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;">random</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10000000</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC156" 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;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">random</span><span class="p">.</span><span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">bad_sect</span><span class="p">(</span><span class="n" style="color: #333;">intlist</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%f for linear (bad) method"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">time</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clock</span></span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">starttime</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%f for linear (bad) method"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">process_time</span></span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">starttime</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_func</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Mapping</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"></span>
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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;">six.moves</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">reduce</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six.moves.collections_abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Mapping</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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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;">bx.misc.binary_file</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">BinaryFileReader</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#afc52934ef927f0b735fed3d6f32f32ede6ea92a"><strong>lib/bx/seq/twobit.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Access to files containing sequence data in 'twobit' format.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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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;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Mapping</span></span>
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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;">struct</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">calcsize</span><span class="p">,</span> <span class="n" style="color: #333;">unpack</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six.moves.collections_abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Mapping</span></span>
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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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_twobit</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">TWOBIT_MAGIC_NUMBER</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x1A412743</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -72,7 +73,7 @@ class TwoBitFile(Mapping):</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">reserved</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;">"L"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Read index of sequence names to offsets</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left right">i</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">seq_count</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">seq_count</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">read_p_string</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;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="s" style="color: #d14;">"L"</span><span class="p">)</span></span>
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78
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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;">index</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TwoBitSequence</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">)</span></span>
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<li id="9e6f610975de2315250d797c93c2336a48af5a4c">
<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#9e6f610975de2315250d797c93c2336a48af5a4c"><strong>scripts/aggregate_scores_in_intervals.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">@@ -16,7 +16,8 @@ from __future__ import division, print_function</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Mapping</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six.moves.collections_abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Mapping</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">bx.wiggle</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">misc</span></span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#5e13d51c89eaefc1a2d15f107f6bf87fb9dc02f8"><strong>scripts/axt_to_lav.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">@@ -153,7 +153,7 @@ def read_lengths(fileName):</td>
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<pre style="margin: 0;"> <span id="LC153" 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 lengths line (%s:%d): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">lineNumber</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chromToLength</span><span class="p">:</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" 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;">"%s appears more than once (%s:%d): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">lineNumber</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC156" 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;">"%s appears more than once (%s:%d): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">lineNumber</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">chromToLength</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#5c685d7860deb9bda05a65dc542b740d20af6718"><strong>scripts/axt_to_maf.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="155" style="width: 35px; color: rgba(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">@@ -155,7 +155,7 @@ def read_lengths(fileName):</td>
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<pre style="margin: 0;"> <span id="LC155" 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 lengths line (%s:%d): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">lineNumber</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></span>
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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="p">(</span><span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chromToLength</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="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;">"%s appears more than once (%s:%d): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">lineNumber</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"%s appears more than once (%s:%d): %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">lineNumber</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">chromToLength</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#dcd8d2010a291b730a1e0a4b6421ea914ae0ec08"><strong>scripts/bed_coverage.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">@@ -9,14 +9,14 @@ usage: %prog bed files ...</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">fileinput</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bx.bitset_builders</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">binned_bitsets_from_file</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">bed_filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bed_filenames</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">chain</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;">bed_filenames</span><span class="p">)<span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fileinput</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">input</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">bed_filenames</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#e17ff8eee288b12833a6a7764b2ae48e0794eebf"><strong>scripts/bed_merge_overlapping.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">@@ -9,14 +9,14 @@ usage: %prog bed files ...</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">fileinput</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">chain</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bx.bitset_builders</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">binned_bitsets_from_bed_file</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">bed_filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bed_filenames</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">chain</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;">bed_filenames</span><span class="p">)<span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fileinput</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">input</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">bed_filenames</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/commit/079d1e351ed66595bd8268f1843a1efe2c1604a5#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">@@ -24,6 +24,8 @@ with open(version_file) as f:</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"Version not found in "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">version_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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="s" style="color: #d14;">'README.md'</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="LC28" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,7 +34,9 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC34" 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;">version</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;">python_requires</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">setup_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cython'</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;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'six'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'six>=1.13.0'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">py_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'psyco_full'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="s" style="color: #d14;">'lib'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'*.ps'</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">@@ -42,7 +46,13 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others"</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;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"james@jamestaylor.org"</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;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Tools for manipulating biological data, particularly multiple sequence alignments"</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;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">long_description</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;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text/markdown'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://github.com/bxlab/bx-python"</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;">project_urls</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"Bug Tracker"</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://github.com/bxlab/bx-python/issues"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">"Source Code"</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://github.com/bxlab/bx-python"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <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;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"MIT"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">"Development Status :: 5 - Production/Stable"</span><span class="p">,</span></span>
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