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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cat-bat">Debian Med / cat-bat</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b">9eb95c03</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-02-11T19:05:36+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.2.3</pre>
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<h4>4 changed files:</h4>
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<a href="#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
CAT_pack/about.py
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<a href="#41cb582341a95a9c89a445c128eaf3fe17244ce8">
CAT_pack/add_names.py
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<li class="file-stats">
<a href="#6bbeca6e8d1075a4925f51d7fc6bc6fb00da58d2">
CAT_pack/prepare.py
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<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<h4>Changes:</h4>
<li id="6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47"><strong>CAT_pack/about.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<pre style="margin: 0;"> <span id="LC3" 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;">'F. A. Bastiaan von Meijenfeldt'</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" 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;">'5.2.<span class="idiff left right">2</span>'</span></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left right">5 Jan</span>uary, 2021'</span></span></pre>
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4
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<pre style="margin: 0;">+<span id="LC4" 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;">'5.2.<span class="idiff left right">3</span>'</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1<span class="idiff left right">0 Febr</span>uary, 2021'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b#41cb582341a95a9c89a445c128eaf3fe17244ce8"><strong>CAT_pack/add_names.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,8 +127,7 @@ def run():</td>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'no taxid found'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span></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;">line</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'no taxid found'</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'no taxid found'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:</span><span class="mi" style="color: #099;">4</span><span class="p">]]):</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ORF has database hits but the accession number is not found</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># in the taxonomy files.</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span 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="n" style="color: #333;">line</span><span class="p">)))</span></span>
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<li id="6bbeca6e8d1075a4925f51d7fc6bc6fb00da58d2">
<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b#6bbeca6e8d1075a4925f51d7fc6bc6fb00da58d2"><strong>CAT_pack/prepare.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" 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">@@ -106,7 +106,7 @@ def download_taxonomy_files(taxonomy_folder, date, log_file, quiet):</td>
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<td class="diff-line-num old_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="s" style="color: #d14;">'taxonomy folder.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">))</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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108
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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;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'</span></span></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;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">{0}taxdump.tar.gz'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">url</span></span><span class="p"><span class="idiff right">)</span></span></span>
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110
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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;">tmp_taxonomy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}{1}.taxdump.tar.gz'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">)</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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112
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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;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_taxonomy_file</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" 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="153" 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">@@ -153,8 +153,7 @@ def download_prot_accession2taxid_file(</td>
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153
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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154
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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155
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/'</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="s" style="color: #d14;">'prot.accession2taxid.FULL.gz'</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="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}prot.accession2taxid.FULL.gz'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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158
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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;">try</span><span class="p">:</span></span>
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159
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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;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">)</span></span>
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160
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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;">except</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,7 +186,7 @@ def download_nr(nr_file, log_file, quiet):</td>
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187
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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188
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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189
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"></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;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz'</span></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;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left">{0}nr.gz'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">url</span></span><span class="p"><span class="idiff right">)</span></span></span>
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191
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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192
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">nr_file</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changelog</span></span>
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2
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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"><span class="gu" style="color: #800080; font-weight: 600;">## 5.2.3</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">Minor bug fix for <span class="sb" style="color: #d14;">`CAT add_names`</span>.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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3
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 5.2.2</span></span>
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4
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">We have added the DIAMOND specific <span class="sb" style="color: #d14;">`--no_self_hits`</span> flag. We have also added some extra checks and removed redundancy from the parser code. Databases constructed by <span class="sb" style="color: #d14;">`CAT prepare`</span> now have a slightly different naming scheme.</span>
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5
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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