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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/metaphlan2">Debian Med / metaphlan2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/metaphlan2/commit/26c497261bed879903b92507a445f91aeb3c9aee">26c49726</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-08T06:22:20Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.9.22</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#b650a02deb9f16531aec1c8085f25f4f1e9942de">
.hg_archival.txt
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<li class="file-stats">
<a href="#fc1a47a75cc8dc593b20b5e840173df634b008a1">
.hgtags
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#816667937d35818eb200780856578a026d986a89">
metaphlan2.py
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<li class="file-stats">
<a href="#9269498522d46f202abf8bc0f2b986c5e07c1d9c">
utils/merge_metaphlan_tables.py
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<li class="file-stats">
<a href="#e6b4cf68fa69a39ac207a783915c8ea4a1fdaece">
utils/read_fastx.py
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<h4>Changes:</h4>
<li id="b650a02deb9f16531aec1c8085f25f4f1e9942de">
<a href="https://salsa.debian.org/med-team/metaphlan2/commit/26c497261bed879903b92507a445f91aeb3c9aee#b650a02deb9f16531aec1c8085f25f4f1e9942de"><strong>.hg_archival.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">repo: 092c2fe2278cb7f0b18d81faeb4aab98b89dc096</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">node: <span class="idiff left right">89633b311684ece67f32a9461aa1567e32dd42f7</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">node: <span class="idiff left right">b16e6ee425dbf3797cc6c222fe0685818921f853</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">branch: 2.9</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">tag: 2.9.2<span class="idiff left right">0</span></span></pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">tag: 2.9.2<span class="idiff left right">2</span></span></pre>
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<li id="fc1a47a75cc8dc593b20b5e840173df634b008a1">
<a href="https://salsa.debian.org/med-team/metaphlan2/commit/26c497261bed879903b92507a445f91aeb3c9aee#fc1a47a75cc8dc593b20b5e840173df634b008a1"><strong>.hgtags</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,3 +36,5 @@ c20357c9133be435919db0b2948f9aa164f19a0b 2.9.15</td>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">71f40111c849408b60e1bc7aeddfef84c9e55eea 2.9.17</span>
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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">170242bd646540bfb5521fe7ff2e54bc8a97dd35 2.9.18</span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">7030c379d395c9eb463ca48943373d52121140d9 2.9.19</span>
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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">89633b311684ece67f32a9461aa1567e32dd42f7 2.9.20</span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">c38b12873d9221abc8c6ade3a1c6fbf808e0c325 2.9.21</span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/metaphlan2/commit/26c497261bed879903b92507a445f91aeb3c9aee#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" 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="69" 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">@@ -69,7 +69,7 @@ MetaPhlAn2 requires *python 2.7* or newer with argparse, tempfile, [numpy](http:</td>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="p">*</span> MetaPhlAn2 is integrated with advanced heatmap plotting with <span class="p">[</span><span class="nv" style="color: #008080;">hclust2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bitbucket.org/nsegata/hclust2</span><span class="p">)</span> and cladogram visualization with <span class="p">[</span><span class="nv" style="color: #008080;">GraPhlAn</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bitbucket.org/nsegata/graphlan/wiki/Home</span><span class="p">)</span>. If you use such visualization tool please refer to their prerequisites. </span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<td class="diff-line-num old old_line" data-linenumber="72" 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="LC72" class="line" lang="markdown">The best way to install MetaPhlAn2 2.9.<span class="idiff left right">15</span> is through conda:</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown">The best way to install MetaPhlAn2 2.9.<span class="idiff left right">20</span> is through conda:</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;">#!bash</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">@@ -96,10 +96,10 @@ You can also install and run MetaPhlAn2 through Docker</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"></span>
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97
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"><span class="p">```</span></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;">#!bash</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>docker pull quay.io/biocontainers/metaphlan2:2.9.<span class="idiff left right">15</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>docker pull quay.io/biocontainers/metaphlan2:2.9.<span class="idiff left right">20</span></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown">Alternatively, you can <span class="gs" style="font-weight: 600;">**manually download**</span> from <span class="p">[</span><span class="nv" style="color: #008080;">Bitbucket</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bitbucket.org/biobakery/metaphlan2/get/2.9.<span class="idiff left right">15</span>.zip</span><span class="p">)</span> or <span class="gs" style="font-weight: 600;">**clone the repository**</span> using the following command <span class="sb" style="color: #d14;">``$ hg clone https://bitbucket.org/biobakery/metaphlan2``</span>.</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">Alternatively, you can <span class="gs" style="font-weight: 600;">**manually download**</span> from <span class="p">[</span><span class="nv" style="color: #008080;">Bitbucket</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bitbucket.org/biobakery/metaphlan2/get/2.9.<span class="idiff left right">20</span>.zip</span><span class="p">)</span> or <span class="gs" style="font-weight: 600;">**clone the repository**</span> using the following command <span class="sb" style="color: #d14;">``$ hg clone https://bitbucket.org/biobakery/metaphlan2``</span>.</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown">If you choose this way, <span class="gs" style="font-weight: 600;">**you'll need to install manually all the dependencies!**</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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="115" 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">@@ -115,7 +115,7 @@ By default, the latest MetaPhlAn2 database is downloaded and built. You can down</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;">#!bash</span></span>
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118
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<td class="diff-line-num new_line old" data-linenumber="118" 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="LC118" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>metaphlan2.py <span class="nt" style="color: #000080;">--install</span> <span class="nt" style="color: #000080;">--index</span> v29_CHOCOPhlAn_201901</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"><span class="nv" style="color: #008080;">$ </span>metaphlan2.py <span class="nt" style="color: #000080;">--install</span> <span class="nt" style="color: #000080;">--index</span> <span class="idiff left right">mpa_</span>v29_CHOCOPhlAn_201901</span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"><span class="p">--------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="612" 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="612" 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">@@ -612,7 +612,7 @@ for f in $(ls fastqs/*.bz2)</td>
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="markdown"><span class="n" style="color: #333;">do</span></span>
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="markdown"> <span class="n" style="color: #333;">echo</span> <span class="s" style="color: #d14;">"Running metaphlan2 on ${f}"</span></span>
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="markdown"> <span class="n" style="color: #333;">bn</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">(</span><span class="n" style="color: #333;">basename</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">f</span><span class="p">}</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">cut</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">d</span> <span class="s" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">f</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="markdown"> <span class="o" style="font-weight: 600;">../</span><span class="n" style="color: #333;">metaphlan2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">index</span> <span class="n" style="color: #333;">v29_CHOCOPhlAn_201901</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">input_type</span> <span class="n" style="color: #333;">multifastq</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">nproc</span> <span class="mi" style="color: #099;">10</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">sams</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">bn</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bz2</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">bowtie2out</span> <span class="n" style="color: #333;">sams</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">bn</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bowtie2_out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bz2</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">o</span> <span class="n" style="color: #333;">ssams</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">bn</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">profile</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">f</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="markdown"> <span class="o" style="font-weight: 600;">../</span><span class="n" style="color: #333;">metaphlan2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">index</span> <span class="n" style="color: #333;"><span class="idiff left right">mpa_</span>v29_CHOCOPhlAn_201901</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">input_type</span> <span class="n" style="color: #333;">multifastq</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">nproc</span> <span class="mi" style="color: #099;">10</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">sams</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">bn</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bz2</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">bowtie2out</span> <span class="n" style="color: #333;">sams</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">bn</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bowtie2_out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bz2</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">o</span> <span class="n" style="color: #333;">ssams</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">bn</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">profile</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="n" style="color: #333;">f</span><span class="p">}</span></span>
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="markdown"><span class="n" style="color: #333;">done</span></span>
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617
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/commit/26c497261bed879903b92507a445f91aeb3c9aee#816667937d35818eb200780856578a026d986a89"><strong>metaphlan2.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">@@ -4,8 +4,8 @@ __author__ = ('Nicola Segata (nicola.segata@unitn.it), '</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="s" style="color: #d14;">'Duy Tin Truong, '</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Asnicar (f.asnicar@unitn.it), '</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="s" style="color: #d14;">'Francesco Beghini (francesco.beghini@unitn.it)'</span><span class="p">)</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.9.2<span class="idiff left right">0</span>'</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" 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;">'14 <span class="idiff left right">Aug</span> 2019'</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.9.2<span class="idiff left right">2</span>'</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" 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;">'14 <span class="idiff left right">Oct</span> 2019'</span></span>
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9
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9
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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="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="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -247,7 +247,7 @@ def read_params(args):</td>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="s" style="color: #d14;">"that 'bowtie2-build is present in the system path"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--bowtie2out'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE_NAME"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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249
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The file for saving the output of BowTie2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--min_mapq_val'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">default</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">5</span></span><span class="p">,</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--min_mapq_val'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">default</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"5"</span></span><span class="p">,</span></span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Minimum mapping quality value (MAPQ)"</span><span class="p">)</span></span>
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252
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--no_map'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Avoid storing the --bowtie2out map file"</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">@@ -526,6 +526,9 @@ def download_unpack_tar(url, download_file_name, folder, bowtie2_build, nproc):</td>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Fatal error running '{}'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Error message: '{}'</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">bt2_cmd</span><span class="p">),</span> <span class="n" style="color: #333;">e</span><span class="p">))</span></span>
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bt2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="n" style="color: #333;">download_file_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"*.bt2"</span><span class="p">)):</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chmod</span><span class="p">(</span><span class="n" style="color: #333;">bt2</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">S_IRUSR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">S_IWUSR</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">S_IRGRP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">S_IWGRP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">S_IROTH</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># change permissions to 664</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python"></span>
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Removing uncompress database {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">fna_file</span><span class="p">))</span></span>
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">fna_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -921,11 +924,11 @@ class TaxTree:</td>
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921
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ignore_eukaryotes</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ignore_bacteria</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ignore_archaea</span><span class="p">:</span></span>
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922
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="python"> <span class="n" style="color: #333;">cn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_full_name</span><span class="p">()</span></span>
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923
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926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ignore_eukaryotes</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"k__Eukaryota"</span><span class="p">):</span></span>
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924
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left right">""</span></span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p"><span class="idiff left">(</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff right">)</span></span></span>
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925
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ignore_archaea</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"k__Archaea"</span><span class="p">):</span></span>
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926
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left right">""</span></span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p"><span class="idiff left">(</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff right">)</span></span></span>
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927
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ignore_bacteria</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"k__Bacteria"</span><span class="p">):</span></span>
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928
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;"><span class="idiff left right">""</span></span></span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p"><span class="idiff left">(</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff right">)</span></span></span>
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929
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># while len(cl.children) == 1:</span></span>
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># cl = list(cl.children.values())[0]</span></span>
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931
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="python"> <span class="n" style="color: #333;">cl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">markers2nreads</span><span class="p">[</span><span class="n" style="color: #333;">marker</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1104" 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">@@ -1104,7 +1107,7 @@ def maybe_generate_biom_file(tree, pars, abundance_predictions):</td>
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1104
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1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">######## clade_ids, #Modified by George Weingart 5/22/2017 - We will use instead the clade_names</span></span>
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1105
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="python"> <span class="n" style="color: #333;">clade_names</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">#Modified by George Weingart 5/22/2017 - We will use instead the clade_names</span></span>
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1106
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="python"> <span class="n" style="color: #333;">sample_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="python"> <span class="n" style="color: #333;">observation_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">to_biomformat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">clade_names</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="python"> <span class="n" style="color: #333;">observation_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">to_biomformat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">clade_names</span></span><span class="p"><span class="idiff right">)</span>),</span></span>
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1108
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="python"> <span class="n" style="color: #333;">table_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_id</span><span class="p">,</span></span>
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1109
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="python"> <span class="n" style="color: #333;">constructor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biom</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DenseOTUTable</span></span>
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1110
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="python"> <span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1118" 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="1121" 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">@@ -1118,7 +1121,7 @@ def maybe_generate_biom_file(tree, pars, abundance_predictions):</td>
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1118
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="python"> <span class="n" style="color: #333;">clade_names</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">#Modified by George Weingart 5/22/2017 - We will use instead the clade_names</span></span>
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1119
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1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="python"> <span class="n" style="color: #333;">sample_ids</span><span class="p">,</span></span>
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1120
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1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="python"> <span class="n" style="color: #333;">sample_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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1121
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<pre style="margin: 0;">-<span id="LC1121" class="line" lang="python"> <span class="n" style="color: #333;">observation_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">to_biomformat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">clade_names</span></span><span class="p">),</span></span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="python"> <span class="n" style="color: #333;">observation_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">to_biomformat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">clade_names</span></span><span class="p"><span class="idiff right">)</span>),</span></span>
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1122
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1125
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="python"> <span class="n" style="color: #333;">table_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table_id</span><span class="p">,</span></span>
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1123
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1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="python"> <span class="n" style="color: #333;">input_is_dense</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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1124
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1127
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="python"> <span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1162" 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">@@ -1159,7 +1162,6 @@ def metaphlan2():</td>
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1159
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1162
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<pre style="margin: 0;"> <span id="LC1162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check for the mpa_pkl file</span></span>
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1160
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1163
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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">'mpa_pkl'</span><span class="p">]):</span></span>
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1161
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1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Unable to find the mpa_pkl file at: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">'mpa_pkl'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>
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1162
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<pre style="margin: 0;">-<span id="LC1162" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Expecting location ${mpa_dir}/db_v20/map_v20_m200.pkl "</span></span>
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1163
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="python"> <span class="s" style="color: #d14;">"Exiting...</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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1164
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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1165
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1167
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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1272" 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">@@ -1270,7 +1272,10 @@ def metaphlan2():</td>
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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">'t'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'rel_ab'</span><span class="p">:</span></span>
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1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">'CAMI_format_output'</span><span class="p">]:</span></span>
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1273
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<pre style="margin: 0;">-<span id="LC1273" class="line" lang="python"> <span class="n" style="color: #333;">outf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'@SampleID:{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">@Version:0.9.1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">@__program__:MetaPhlAn{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">@Ranks:superkingdom|phylum|class|order|family|genus|species</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">@@TAXID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">RANK</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TAXPATH</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TAXPATHSN</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PERCENTAGE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">"sample_id"</span><span class="p">],</span><span class="n" style="color: #333;">__version__</span><span class="p">))</span></span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="python"> <span class="n" style="color: #333;">outf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"@SampleID:{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="python"> <span class="s" style="color: #d14;">"@Version:0.10.0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="python"> <span class="s" style="color: #d14;">"@Ranks:superkingdom|phylum|class|order|family|genus|species|strain</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="python"> <span class="s" style="color: #d14;">"@@TAXID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">RANK</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TAXPATH</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TAXPATHSN</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PERCENTAGE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">"sample_id"</span><span class="p">],</span><span class="n" style="color: #333;">__version__</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">'legacy_output'</span><span class="p">]:</span></span>
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="python"> <span class="n" style="color: #333;">outf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'#clade_name</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NCBI_tax_id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">relative_abundance</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1289" 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="1294" 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">@@ -1289,7 +1294,7 @@ def metaphlan2():</td>
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1294
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxid</span><span class="p">:</span></span>
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1295
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="python"> <span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ranks2code</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span></span>
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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="python"> <span class="n" style="color: #333;">leaf_taxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxid</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC1292" class="line" lang="python"> <span class="n" style="color: #333;">taxpathsh</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">remove_prefix</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="python"> <span class="n" style="color: #333;">taxpathsh</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">remove_prefix</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'_unclassified'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">''</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="p">)])</span></span>
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1293
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1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="python"> <span class="n" style="color: #333;">outf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="p">[</span> <span class="n" style="color: #333;">leaf_taxid</span><span class="p">,</span> <span class="n" style="color: #333;">rank</span><span class="p">,</span> <span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">taxpathsh</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">relab</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fraction_mapped_reads</span><span class="p">)</span> <span class="p">]</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="p">)</span></span>
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pars</span><span class="p">[</span><span class="s" style="color: #d14;">'unknown_estimation'</span><span class="p">]:</span></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/commit/26c497261bed879903b92507a445f91aeb3c9aee#9269498522d46f202abf8bc0f2b986c5e07c1d9c"><strong>utils/merge_metaphlan_tables.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">@@ -39,7 +39,7 @@ def merge( aaastrIn, ostm ):</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">listmpaVersion</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'merge_metaphlan_tables found tables made with different versions of the MetaPhlAn2 database.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Please re-run MetaPhlAn2 with the same database.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">iIn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">skiprows</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">headers</span><span class="p">),</span></span>
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<a href="https://salsa.debian.org/med-team/metaphlan2/commit/26c497261bed879903b92507a445f91aeb3c9aee#e6b4cf68fa69a39ac207a783915c8ea4a1fdaece"><strong>utils/read_fastx.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" 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">@@ -101,6 +101,12 @@ def read_and_write_raw_int(fd, min_len=None):</td>
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101
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<pre style="margin: 0;"> <span id="LC101" 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="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">ignore_spaces</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Read again the first line of the file to determine if is a fasta or a fastq</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">fd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">readn</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fastx</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'fastq'</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">//</span> <span class="n" style="color: #333;">readn</span></span>
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104
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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105
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">nreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">discarded</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nreads</span></span>
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