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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/resfinder">Debian Med / resfinder</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/resfinder/commit/ef10b47463acad3a6d4264c8968345ff8b83b27a">ef10b474</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-07T11:41:12Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#c756979c7dd1b0c19afe60cc8a94e9d648f31bdf">
resfinder.py
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/resfinder/commit/ef10b47463acad3a6d4264c8968345ff8b83b27a#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +66,7 @@ You can run resfinder command line using python3</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(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="LC67" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Example of running resfinder</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown">python3 resfinder.py <span class="nt" style="color: #000080;">-i</span> test.fsa <span class="nt" style="color: #000080;">-o</span> <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-p</span> /path/to/resfinder_db <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"><span class="nt" style="color: #000080;">-b</span> /path/to/blastn <span class="nt" style="color: #000080;">-d</span> aminoglycoside <span class="nt" style="color: #000080;">-<span class="idiff left">k</span></span><span class="idiff right"> 90.0</span>0 <span class="nt" style="color: #000080;">-l</span> 0.60</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="nt" style="color: #000080;">-b</span> /path/to/blastn <span class="nt" style="color: #000080;">-d</span> aminoglycoside <span class="nt" style="color: #000080;">-<span class="idiff left">t</span></span><span class="idiff right"> 0.9</span>0 <span class="nt" style="color: #000080;">-l</span> 0.60</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># The program can be invoked with the -h option </span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown">Usage: resfinder.py <span class="o" style="font-weight: 600;">[</span><span class="nt" style="color: #000080;">-h</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">[</span><span class="nt" style="color: #000080;">-i</span> INPUTFILE] <span class="o" style="font-weight: 600;">[</span><span class="nt" style="color: #000080;">-1</span> FASTQ1] <span class="o" style="font-weight: 600;">[</span><span class="nt" style="color: #000080;">-2</span> FASTQ2] <span class="o" style="font-weight: 600;">[</span><span class="nt" style="color: #000080;">-o</span> OUT_PATH]</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(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="103" style="width: 35px; color: rgba(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">@@ -103,6 +103,10 @@ optional arguments:</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-t</span> THRESHOLD, <span class="nt" style="color: #000080;">--threshold</span> THRESHOLD</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"> Blast threshold <span class="k" style="font-weight: 600;">for </span>identity</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"> default minimum 0.9 </span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"> <span class="nt" style="color: #000080;">-matrix</span>, <span class="nt" style="color: #000080;">--matrix</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"> If used, gives the counts all all called bases at each position</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">in </span>each mapped template. Columns are: reference base,</span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC109" class="line" lang="markdown"> A count, C count, G count, T count, N count, - count.</span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Web-server</span></span>
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<li id="c756979c7dd1b0c19afe60cc8a94e9d648f31bdf">
<a href="https://salsa.debian.org/med-team/resfinder/commit/ef10b47463acad3a6d4264c8968345ff8b83b27a#c756979c7dd1b0c19afe60cc8a94e9d648f31bdf"><strong>resfinder.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,10 @@ import subprocess</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tabulate</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tabulate</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;">collections</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pprint</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">json</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.spawn</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">find_executable</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cgecore.blaster</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Blaster</span></span>
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14
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cgecore.cgefinder</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CGEFinder</span></span>
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15
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +31,7 @@ class ResFinder(CGEFinder):</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">db_path_kma</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">db_path_kma</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configured_dbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description_dbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kma_db_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_db_config</span><span class="p">(</span><span class="n" style="color: #333;">db_conf_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_conf_file</span><span class="p">)</span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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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="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,288 +40,311 @@ class ResFinder(CGEFinder):</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">phenos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_notes</span><span class="p">(</span><span class="n" style="color: #333;">notes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">notes</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">blast_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.kma_results = None</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.results = None</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_results</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">res_type</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_BLAST</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">result_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">results_to_str</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">res_type</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">results</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">query_align</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_align_query</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">homo_align</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_align_homo</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_align</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_align_sbjct</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_KMA</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">result_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">results_to_str</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">res_type</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/results_tab.txt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">fh</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;">result_str</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="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/results_table.txt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">fh</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;">result_str</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/results.txt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">fh</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;">result_str</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/Resistance_gene_seq.fsa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">fh</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;">result_str</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/Hit_in_genome_seq.fsa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">fh</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;">result_str</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="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">blast</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="n" style="color: #333;">min_cov</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.9</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.6</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">blast</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"blastn"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">blast</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"blastn"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allowed_overlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">blast_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Blaster</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">databases</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">databases</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">db_path</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_path</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">min_cov</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min_cov</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="n" style="color: #333;">blast</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blast</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">min_cov</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min_cov</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="n" style="color: #333;">blast</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blast</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">allowed_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">allowed_overlap</span><span class="p">)</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">blast_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blast_run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">results</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">blast_run</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">results_to_str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">res_type</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">,</span> <span class="n" style="color: #333;">query_align</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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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">homo_align</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">sbjct_align</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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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_results</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">results_method</span><span class="p">,</span><span class="n" style="color: #333;">outdir</span><span class="p">):</span></span>
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80
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_BLAST</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_KMA</span><span class="p">):</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="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="s" style="color: #d14;">"resfinder.py error: result method was not provided or not "</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"recognized."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_method</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">results</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">query_aligns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_method</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_align_query</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">homo_aligns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_method</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_align_homo</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_aligns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results_method</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gene_align_sbjct</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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84
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write the header for the tab file</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">tab_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"Resistance gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Identity</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Alignment Length/Gene Length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"Coverage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Position in reference</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Contig</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">"Position in contig</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Phenotype</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Accession no.</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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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">table_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">ref_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">hit_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Getting and writing out the results</span></span>
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96
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">titles</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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97
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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98
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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99
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">txt_file_seq_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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100
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">split_print</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>
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101
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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102
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"excluded"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Clean up dbs with only excluded hits</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;">no_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]:</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="s" style="color: #d14;">"excluded"</span><span class="p">]):</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"hit not excluded: "</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;">hit</span><span class="p">))</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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;">In DB: "</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;">db</span><span class="p">))</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">no_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">no_hits</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"No hits in: "</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;">db</span><span class="p">))</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"No hit found"</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">profile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configured_dbs</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"No hit found"</span><span class="p">:</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">table_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">profile</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]))</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">titles</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">profile</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Resistance gene"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Identity"</span><span class="p">,</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="s" style="color: #d14;">"Alignment Length/Gene Length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Coverage"</span><span class="p">,</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"Position in reference"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Contig"</span><span class="p">,</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"Position in contig"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Phenotype"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">"Accession no."</span><span class="p">]</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">table_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">profile</span><span class="p">))</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">table_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"Resistance gene</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Identity</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="130" 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">
130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="s" style="color: #d14;">"Alignment Length/Gene Length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Coverage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="s" style="color: #d14;">"Position in reference</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Contig</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Position in contig</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="s" style="color: #d14;">"Phenotype</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Accession no.</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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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">txt_file_seq_text</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]:</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="s" style="color: #d14;">"excluded"</span><span class="p">]):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">contig_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'excluded'</span><span class="p">:</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">db_name</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;">db</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">capitalize</span><span class="p">()</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">db_name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">json_results</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"No hit found"</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"No hit found"</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig_id</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">identity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"perc_ident"</span><span class="p">])</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"perc_coverage"</span><span class="p">])</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Skip hits below coverage</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">min_cov</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">):</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">bit_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">identity</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coverage</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contig_id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_res</span><span class="p">:</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">contig_res</span><span class="p">[</span><span class="n" style="color: #333;">contig_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">contig_res</span><span class="p">[</span><span class="n" style="color: #333;">contig_id</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_start"</span><span class="p">],</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_end"</span><span class="p">],</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">bit_score</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">])</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check for overlapping hits, only report the best</span></span>
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102
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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;">contig_id</span><span class="p">,</span> <span class="n" style="color: #333;">hit_lsts</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</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>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">hit_lsts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hit_lsts</span><span class="p">]</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hit</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hits</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"sbjct_header"</span><span class="p">]</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</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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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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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</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="LC113" class="line" lang="python"> <span class="n" style="color: #333;">note</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">acc</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;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IndexError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">gene</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;">tmp</span><span class="p">)</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">note</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IndexError</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">identity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"perc_ident"</span><span class="p">]</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"perc_coverage"</span><span class="p">]</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">sbj_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"sbjct_length"</span><span class="p">]</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">HSP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"HSP_length"</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">positions_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s..</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_start"</span><span class="p">],</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"query_end"</span><span class="p">])</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s..</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"sbjct_start"</span><span class="p">],</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"sbjct_end"</span><span class="p">])</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;">contig_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hit</span><span class="p">[</span><span class="s" style="color: #d14;">"contig_name"</span><span class="p">]</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">phenos</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: gene is missing from "</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="s" style="color: #d14;">"Notes file. Please inform curator."</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write JSON results dict</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="n" style="color: #333;">header</span><span class="p">:</span> <span class="p">{}})</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">json_results</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">header</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">"resistance_gene"</span><span class="p">:</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">"identity"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">identity</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">"HSP_length"</span><span class="p">:</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">"template_length"</span><span class="p">:</span> <span class="n" style="color: #333;">sbj_length</span><span class="p">,</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="s" style="color: #d14;">"position_in_ref"</span><span class="p">:</span> <span class="n" style="color: #333;">positions_ref</span><span class="p">,</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="s" style="color: #d14;">"contig_name"</span><span class="p">:</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"positions_in_contig"</span><span class="p">:</span> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"note"</span><span class="p">:</span> <span class="n" style="color: #333;">note</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">"accession"</span><span class="p">:</span> <span class="n" style="color: #333;">acc</span><span class="p">,</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"predicted_phenotype"</span><span class="p">:</span> <span class="n" style="color: #333;">pheno</span><span class="p">,</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">"coverage"</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">"hit_id"</span><span class="p">:</span> <span class="n" style="color: #333;">contig_id</span><span class="p">}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get run info for JSON file</span></span>
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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;">service</span> <span class="o" style="font-weight: 600;">=</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;">basename</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">".py"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">date</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">m.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">Y"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">time_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">H:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">M:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">S"</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>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make JSON output file</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">service</span><span class="p">:</span> <span class="p">{}}</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">userinput</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"filename(s)"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="s" style="color: #d14;">"method"</span><span class="p">:</span> <span class="n" style="color: #333;">method</span><span class="p">,</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="s" style="color: #d14;">"file_format"</span><span class="p">:</span> <span class="n" style="color: #333;">file_format</span><span class="p">}</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">run_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">date</span><span class="p">,</span> <span class="s" style="color: #d14;">"time"</span><span class="p">:</span> <span class="n" style="color: #333;">time_</span><span class="p">}</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"user_input"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">userinput</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"run_info"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_info</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">service</span><span class="p">][</span><span class="s" style="color: #d14;">"results"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json_results</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">pprint</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pprint</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Save json output</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">result_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}/data_resfinder.json"</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;">tmp_dir</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">result_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outfile</span><span class="p">:</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Getting and writing out the results</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Resistance gene"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Identity"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Query / Template length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Contig"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">"Position in contig"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Predicted phenotype"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Accession number"</span><span class="p">]</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extented_output</span><span class="p">:</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define extented output</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">table_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}/results_tab.tsv"</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;">outdir</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">query_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}/Hit_in_genome_seq.fsa"</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;">outdir</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}/Resistance_genes.fsa"</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;">outdir</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">result_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}/results.txt"</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;">outdir</span><span class="p">)</span></span>
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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;">table_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">table_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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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;">query_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">query_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">sbjct_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">result_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">result_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Make results file</span></span>
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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;">result_file</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;">"{} Results</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Antibiotic(s): {}</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <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;">service</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configured_dbs</span><span class="p">)))</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write tsv table</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">## TODO##</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="s" style="color: #d14;">"Database"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">header</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">species</span><span class="p">,</span> <span class="n" style="color: #333;">dbs_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">json_results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">db_name</span><span class="p">,</span> <span class="n" style="color: #333;">db_hits</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dbs_info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">result_file</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="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</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="n" style="color: #333;">header</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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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">result_file</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;">db_name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">capitalize</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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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">db_rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check it hits are found</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">db_hits</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">content</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">''</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">content</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">db_hits</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">([</span><span class="n" style="color: #333;">content</span><span class="p">])</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">result_file</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;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text_table</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">content</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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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene_id</span><span class="p">,</span> <span class="n" style="color: #333;">gene_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">db_hits</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="s" style="color: #d14;">'resistance_gene'</span><span class="p">],</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="s" style="color: #d14;">'accession'</span><span class="p">])):</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">res_gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"resistance_gene"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">identity</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;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"identity"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">coverage</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;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"coverage"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">template_HSP</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="s" style="color: #d14;">"{hsp_len} / {template_len}"</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">hsp_len</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"HSP_length"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">template_len</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"template_length"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">position_in_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"position_in_ref"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">position_in_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"positions_in_contig"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">predicted_phenotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"predicted_phenotype"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"accession"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">contig_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"contig_name"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">contig_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add rows to result tables</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">db_rows</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">res_gene</span><span class="p">,</span> <span class="n" style="color: #333;">identity</span><span class="p">,</span> <span class="n" style="color: #333;">template_HSP</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">position_in_contig</span><span class="p">,</span> <span class="n" style="color: #333;">predicted_phenotype</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">])</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">rows</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">db_name</span><span class="p">,</span> <span class="n" style="color: #333;">res_gene</span><span class="p">,</span> <span class="n" style="color: #333;">identity</span><span class="p">,</span> <span class="n" style="color: #333;">template_HSP</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span> <span class="n" style="color: #333;">position_in_contig</span><span class="p">,</span> <span class="n" style="color: #333;">predicted_phenotype</span><span class="p">,</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">acc</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write query fasta output</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">hit_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"hit_id"</span><span class="p">]</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">query_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query_aligns</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">hit_name</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sbjct_aligns</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">hit_name</span><span class="p">]</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">identity</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PERFECT MATCH"</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"WARNING"</span></span>
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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;">qry_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">">{}:{} ID:{}</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">COV:{}</span><span class="si" style="color: #d14;">% </span><span class="s" style="color: #d14;">Best_match:{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <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;">res_gene</span><span class="p">,</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">identity</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</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;">gene_id</span><span class="p">))</span></span>
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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;">query_file</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;">qry_header</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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">query_seq</span><span class="p">),</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">query_file</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;">query_seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</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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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write template fasta output</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">sbj_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_file</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;">sbj_header</span><span class="p">)</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sbjct_seq</span><span class="p">),</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_file</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;">sbjct_seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</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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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write db results tables in results file and table file</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">db_rows</span><span class="p">)</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">result_file</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;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text_table</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">db_rows</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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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">result_file</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;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span><span class="p">:</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">table_file</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="n" style="color: #333;">row</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write allignment output</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">result_file</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;">\n\n</span><span class="s" style="color: #d14;">Extended Output:</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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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">make_aln</span><span class="p">(</span><span class="n" style="color: #333;">result_file</span><span class="p">,</span> <span class="n" style="color: #333;">json_results</span><span class="p">,</span> <span class="n" style="color: #333;">query_aligns</span><span class="p">,</span> <span class="n" style="color: #333;">homo_aligns</span><span class="p">,</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_aligns</span><span class="p">)</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Close all files</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">query_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">table_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">result_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_aln</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">file_handle</span><span class="p">,</span> <span class="n" style="color: #333;">json_data</span><span class="p">,</span> <span class="n" style="color: #333;">query_aligns</span><span class="p">,</span> <span class="n" style="color: #333;">homol_aligns</span><span class="p">,</span> <span class="n" style="color: #333;">sbjct_aligns</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">dbs_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">json_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">db_name</span><span class="p">,</span> <span class="n" style="color: #333;">db_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dbs_info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">db_info</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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139
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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140
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">res_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"sbjct_header"</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res_header</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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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">acc</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;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"perc_ident"</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"perc_coverage"</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">sbjt_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"sbjct_length"</span><span class="p">]</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">HSP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"HSP_length"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">positions_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s..</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"query_start"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"query_end"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s..</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"sbjct_start"</span><span class="p">],</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"sbjct_end"</span><span class="p">])</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">contig_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"contig_name"</span><span class="p">]</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">phenos</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: gene is missing from "</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">"Notes file. Please inform curator."</span><span class="p">)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene_id</span><span class="p">,</span> <span class="n" style="color: #333;">gene_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">db_info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="s" style="color: #d14;">'resistance_gene'</span><span class="p">],</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="s" style="color: #d14;">'accession'</span><span class="p">])):</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">seq_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"{gene}_{acc}"</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <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;">gene</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"resistance_gene"</span><span class="p">],</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">acc</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"accession"</span><span class="p">]))</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">hit_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_info</span><span class="p">[</span><span class="s" style="color: #d14;">"hit_id"</span><span class="p">]</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">]</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sbjct_aligns</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">hit_name</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homol_aligns</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">hit_name</span><span class="p">]</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query_aligns</span><span class="p">[</span><span class="n" style="color: #333;">db_name</span><span class="p">][</span><span class="n" style="color: #333;">hit_name</span><span class="p">]</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_align</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seq_name</span><span class="p">,</span> <span class="n" style="color: #333;">file_handle</span><span class="p">)</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_align</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seq_name</span><span class="p">,</span> <span class="n" style="color: #333;">file_handle</span><span class="p">):</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">file_handle</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="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">seq_name</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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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">homol_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">query_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sbjct_seq</span><span class="p">),</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">file_handle</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="si" style="color: #d14;">%-10</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="s" style="color: #d14;">"template:"</span><span class="p">,</span> <span class="n" style="color: #333;">sbjct_seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">file_handle</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="si" style="color: #d14;">%-10</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">homol_seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">file_handle</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="si" style="color: #d14;">%-10</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="s" style="color: #d14;">"query:"</span><span class="p">,</span> <span class="n" style="color: #333;">query_seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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156
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"split_length"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">total_HSP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"split_length"</span><span class="p">]</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res_header</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">total_HSP</span><span class="p">,</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">sbjt_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span> <span class="n" style="color: #333;">pheno</span><span class="p">,</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">acc</span><span class="p">])</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">tab_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span> <span class="n" style="color: #333;">sbjt_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="p">)</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write tabels</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">table_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.2</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span> <span class="n" style="color: #333;">sbjt_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span> <span class="n" style="color: #333;">pheno</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="p">)</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">tab_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.2</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="LC179" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span> <span class="n" style="color: #333;">sbjt_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="p">)</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Saving the output to write the txt result table</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">hsp_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">HSP</span><span class="p">,</span> <span class="n" style="color: #333;">sbjt_length</span><span class="p">)</span></span>
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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;">rows</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">hsp_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span></span>
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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;">positions_ref</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">])</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Writing subjet/ref sequence</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_BLAST</span><span class="p">):</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">ref_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sbjct_align</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">]</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_KMA</span><span class="p">):</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">ref_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"sbjct_string"</span><span class="p">]</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">ref_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"></span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">))</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ref_seq</span><span class="p">),</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">ref_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">ref_seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Getting the header and text for the txt file output</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"sbjct_start"</span><span class="p">]</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"sbjct_end"</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, ID: </span><span class="si" style="color: #d14;">%.2</span><span class="s" style="color: #d14;">f </span><span class="si" style="color: #d14;">%%</span><span class="s" style="color: #d14;">, Alignment Length/Gene Length: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, "</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">"Coverage: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, "</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">"Positions in reference: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s..</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, Contig name: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, "</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">"Position: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span> <span class="n" style="color: #333;">sbjt_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">sbjct_start</span><span class="p">,</span> <span class="n" style="color: #333;">sbjct_end</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">positions_contig</span><span class="p">))</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">hit_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"></span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="n" style="color: #333;">text</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Writing query/hit sequence</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_BLAST</span><span class="p">):</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">hit_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query_align</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">]</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_KMA</span><span class="p">):</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">hit_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"query_string"</span><span class="p">]</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">hit_seq</span><span class="p">),</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">hit_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">hit_seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Saving the output to print the txt result file allignemts</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_BLAST</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">txt_file_seq_text</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">homo_align</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">],</span> <span class="n" style="color: #333;">hit_seq</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span><span class="p">(</span><span class="n" style="color: #333;">res_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_KMA</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">txt_file_seq_text</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">][</span><span class="n" style="color: #333;">hit</span><span class="p">][</span><span class="s" style="color: #d14;">"homo_string"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">hit_seq</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">split_print</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">HSP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">sbjt_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">contig_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">positions_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">7</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">8</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">9</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">total_coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">])):</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, </span><span class="si" style="color: #d14;">%.2</span><span class="s" style="color: #d14;">f"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">total_coverage</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="n" style="color: #333;">i</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="LC246" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">positions_ref</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;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">contig_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contig_name</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;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">6</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;">positions_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">positions_contig</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", "</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">split_print</span><span class="p">[</span><span class="n" style="color: #333;">res</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">7</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">table_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="LC252" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">HSP</span><span class="p">,</span> <span class="n" style="color: #333;">sbjt_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">positions_ref</span><span class="p">,</span> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">pheno</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">hsp_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s/</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">HSP</span><span class="p">,</span> <span class="n" style="color: #333;">sbjt_length</span><span class="p">)</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">,</span> <span class="n" style="color: #333;">hsp_length</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">,</span> <span class="n" style="color: #333;">positions_ref</span><span class="p">,</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">contig_name</span><span class="p">,</span> <span class="n" style="color: #333;">positions_contig</span><span class="p">,</span> <span class="n" style="color: #333;">pheno</span><span class="p">,</span> <span class="n" style="color: #333;">acc</span><span class="p">])</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">table_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Writing table txt for all hits</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">titles</span><span class="p">:</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Txt file table</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text_table</span><span class="p">(</span><span class="n" style="color: #333;">titles</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">],</span> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">],</span> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">])</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">table</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Writing alignment txt for all hits</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">db</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">titles</span><span class="p">:</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Txt file alignments</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"##################### </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s #####################</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">))</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">text</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">txt_file_seq_text</span><span class="p">[</span><span class="n" style="color: #333;">db</span><span class="p">]:</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">text</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="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">text</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">text</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="p">(</span><span class="n" style="color: #333;">text</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">60</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">txt_str</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">tab_str</span><span class="p">,</span> <span class="n" style="color: #333;">table_str</span><span class="p">,</span> <span class="n" style="color: #333;">txt_str</span><span class="p">,</span> <span class="n" style="color: #333;">ref_str</span><span class="p">,</span> <span class="n" style="color: #333;">hit_str</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">text_table</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">table_format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'psql'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="s" style="color: #d14;">''' Create text table</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;"> USAGE:</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from tabulate import tabulate</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;"> >>> title = 'My Title'</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"><span class="s" style="color: #d14;"> >>> headers = ['A','B']</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;"> >>> rows = [[1,2],[3,4]]</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;"> >>> print(text_table(title, headers, rows))</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"><span class="s" style="color: #d14;"> +-----------+</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;"> | My Title |</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;"> +-----+-----+</span></span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"><span class="s" style="color: #d14;"> | A | B |</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"><span class="s" style="color: #d14;"> +=====+=====+</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"><span class="s" style="color: #d14;"> | 1 | 2 |</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"><span class="s" style="color: #d14;"> | 3 | 4 |</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"><span class="s" style="color: #d14;"> +-----+-----+</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create table</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tabulate</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">tablefmt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">table_format</span><span class="p">)</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Prepare title injection</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">width</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;">table</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">tlen</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;">title</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tlen</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">width</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Truncate oversized titles</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">tlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">title</span><span class="p">[:</span><span class="n" style="color: #333;">tlen</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">spaces</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tlen</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">left_spacer</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">spaces</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">right_spacer</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="p">(</span><span class="n" style="color: #333;">spaces</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;">left_spacer</span><span class="p">))</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Update table with title</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">table</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'+</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s+'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">'-'</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">)),</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="s" style="color: #d14;">'|</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s|'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">left_spacer</span><span class="p">,</span> <span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">right_spacer</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">text_table</span><span class="p">(</span><span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">empty_replace</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'-'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="s" style="color: #d14;">''' Create text table</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"><span class="s" style="color: #d14;"> USAGE:</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"><span class="s" style="color: #d14;"> >>> from tabulate import tabulate</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"><span class="s" style="color: #d14;"> >>> headers = ['A','B']</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"><span class="s" style="color: #d14;"> >>> rows = [[1,2],[3,4]]</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"><span class="s" style="color: #d14;"> >>> print(text_table(headers, rows))</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"><span class="s" style="color: #d14;"> **********</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"><span class="s" style="color: #d14;"> A B</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"><span class="s" style="color: #d14;"> **********</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"><span class="s" style="color: #d14;"> 1 2</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"><span class="s" style="color: #d14;"> 3 4</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"><span class="s" style="color: #d14;"> ==========</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Replace empty cells with placeholder</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">row</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">empty_replace</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">),</span> <span class="n" style="color: #333;">rows</span><span class="p">)</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create table</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tabulate</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">tablefmt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'simple'</span><span class="p">)</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="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="LC340" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Prepare title injection</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">width</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;">table</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Switch horisontal line</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Update table with title</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</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="mi" style="color: #099;">3</span><span class="p">)</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="s" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">),</span> <span class="s" style="color: #d14;">'='</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_notes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">notes</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">notes</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(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="417" style="width: 35px; color: rgba(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">@@ -390,6 +417,7 @@ class ResFinder(CGEFinder):</td>
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390
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">db_prefix</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configured_dbs</span><span class="p">:</span></span>
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391
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configured_dbs</span><span class="p">[</span><span class="n" style="color: #333;">db_prefix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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392
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configured_dbs</span><span class="p">[</span><span class="n" style="color: #333;">db_prefix</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description_dbs</span><span class="p">[</span><span class="n" style="color: #333;">db_prefix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">description</span></span>
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393
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"></span>
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394
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422
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<pre style="margin: 0;"> <span id="LC422" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">configured_dbs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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395
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423
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<pre style="margin: 0;"> <span id="LC423" 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="s" style="color: #d14;">"Input Error: No databases were found in the "</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="401" style="width: 35px; color: rgba(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="429" style="width: 35px; color: rgba(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">@@ -401,6 +429,52 @@ class ResFinder(CGEFinder):</td>
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401
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kma_db_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">kma_db</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".b"</span><span class="p">,</span> <span class="n" style="color: #333;">kma_db</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".length.b"</span><span class="p">,</span></span>
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402
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">kma_db</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".name.b"</span><span class="p">,</span> <span class="n" style="color: #333;">kma_db</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".align.b"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_gzipped</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="s" style="color: #d14;">''' Returns True if file is gzipped and False otherwise.</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"><span class="s" style="color: #d14;"> The result is inferred from the first two bits in the file read</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"><span class="s" style="color: #d14;"> from the input path.</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"><span class="s" style="color: #d14;"> On unix systems this should be: 1f 8b</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"><span class="s" style="color: #d14;"> Theoretically there could be exceptions to this test but it is</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"><span class="s" style="color: #d14;"> unlikely and impossible if the input files are otherwise expected</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"><span class="s" style="color: #d14;"> to be encoded in utf-8.</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"><span class="s" style="color: #d14;"> '''</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">bit_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bit_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\x1f\x8b</span><span class="s" style="color: #d14;">'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC445" 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="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_file_format</span><span class="p">(</span><span class="n" style="color: #333;">input_files</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"><span class="s" style="color: #d14;"> Takes all input files and checks their first character to assess</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"><span class="s" style="color: #d14;"> the file format. Returns one of the following strings; fasta, fastq,</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"><span class="s" style="color: #d14;"> other or mixed. fasta and fastq indicates that all input files are</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"><span class="s" style="color: #d14;"> of the same format, either fasta or fastq. other indiates that all</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"><span class="s" style="color: #d14;"> files are not fasta nor fastq files. mixed indicates that the inputfiles</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"><span class="s" style="color: #d14;"> are a mix of different file formats.</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Open all input files and get the first character</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">invalid_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">infile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">input_files</span><span class="p">:</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_gzipped</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">):</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzip</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">fst_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">fst_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Assess the first character</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fst_char</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">"@"</span><span class="p">:</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">file_format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"fastq"</span><span class="p">)</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">fst_char</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">">"</span><span class="p">:</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="n" style="color: #333;">file_format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" 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="LC474" class="line" lang="python"> <span class="n" style="color: #333;">invalid_files</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"other"</span><span class="p">)</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">file_format</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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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"mixed"</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">file_format</span><span class="p">))</span></span>
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404
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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406
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480
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<pre style="margin: 0;"> <span id="LC480" 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">@@ -411,41 +485,26 @@ if __name__ == '__main__':</td>
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485
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">()</span></span>
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412
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486
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--inputfile"</span><span class="p">,</span></span>
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"inputfile"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC414" 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;">"Input file"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <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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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--fastq1"</span><span class="p">,</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" 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;">"Raw read data file 1."</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">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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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--fastq2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC420" 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;">"Raw read data file 2 (only required if data is </span><span class="se" style="color: #d14;">\</span></span>
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421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"><span class="s" style="color: #d14;"> paired-end)."</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"> <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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488
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<pre style="margin: 0;">+<span id="LC488" 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;">"FASTA or FASTQ input files."</span><span class="p">,</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"+"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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423
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--outputPath"</span><span class="p">,</span></span>
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424
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"out_path"</span><span class="p">,</span></span>
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425
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493
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<pre style="margin: 0;"> <span id="LC493" 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;">"Path to blast output"</span><span class="p">,</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'.'</span><span class="p">)</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-tmp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--tmp_dir"</span><span class="p">,</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"Temporary directory for storage of the results "</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="s" style="color: #d14;">"from the external software."</span><span class="p">))</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-mp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--methodPath"</span><span class="p">,</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"method_path"</span><span class="p">,</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" 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;">"Path to method to use (kma or blastn)"</span><span class="p">)</span></span>
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427
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"></span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--blastPath"</span><span class="p">,</span></span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"blast_path"</span><span class="p">,</span></span>
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430
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<td class="diff-line-num new_line old" data-linenumber="503" 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="LC430" 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;">"Path to blast"</span><span class="p">,</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'blastn'</span><span class="p">)</span></span>
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432
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--databasePath"</span><span class="p">,</span></span>
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433
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"db_path"</span><span class="p">,</span></span>
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434
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505
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<pre style="margin: 0;"> <span id="LC505" 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;">"Path to the databases"</span><span class="p">,</span></span>
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435
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-k"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--kmaPath"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"kma_path"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Path to KMA"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <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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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--databasePathKMA"</span><span class="p">,</span></span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"db_path_kma"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Path to the directories containing the KMA </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"><span class="s" style="color: #d14;"> indexed databases. Defaults to the directory </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"><span class="s" style="color: #d14;"> 'kma_indexing' inside the databasePath </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"><span class="s" style="color: #d14;"> directory."</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <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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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--databases"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"databases"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC510" 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;">"Databases chosen to search in - if none are </span><span class="se" style="color: #d14;">\</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">@@ -459,16 +518,45 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"threshold"</span><span class="p">,</span></span>
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519
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<pre style="margin: 0;"> <span id="LC519" 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;">"Blast threshold for identity"</span><span class="p">,</span></span>
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.90</span><span class="p">)</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-ao"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--acq_overlap"</span><span class="p">,</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Genes are allowed to overlap this number of</span><span class="se" style="color: #d14;">\</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"><span class="s" style="color: #d14;"> nucleotides. Default: 30."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">30</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-matrix"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--matrix"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC527" 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;">"Gives the counts all all called bases at each</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="python"><span class="s" style="color: #d14;"> position in each mapped template. Columns are: reference</span><span class="se" style="color: #d14;">\</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"><span class="s" style="color: #d14;"> base, A count, C count, G count, T count, N count,</span><span class="se" style="color: #d14;">\</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python"><span class="s" style="color: #d14;"> - count."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"kma_matrix"</span><span class="p">,</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python"> <span class="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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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-x"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--extented_output"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"Give extented output with allignment files, "</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="s" style="color: #d14;">"template and query hits in fasta and a tab "</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"> <span class="s" style="color: #d14;">"seperated file with gene profile results"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"> <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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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--quiet"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">##########################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># MAIN</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">##########################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'/dev/null'</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC551" 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;">stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Defining varibales</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">min_cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_cov</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threshold</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="n" style="color: #333;">min_cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_cov</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threshold</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">method_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">method_path</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if valid database is provided</span></span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">db_path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="489" style="width: 35px; color: rgba(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">@@ -489,37 +577,17 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC577" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">notes_path</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC578" 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="s" style="color: #d14;">'Input Error: notes.txt not found! (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">notes_path</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check for input</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastq1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC494" 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="s" style="color: #d14;">"Input Error: No Input were provided!</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="LC495" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if valid input file for assembly is provided</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC498" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC499" 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="s" style="color: #d14;">"Input Error: Input file does not exist!</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="LC500" 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="LC501" class="line" lang="python"> <span class="n" style="color: #333;">inputfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span></span>
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<pre style="margin: 0;">-<span id="LC502" 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="LC503" class="line" lang="python"> <span class="n" style="color: #333;">inputfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if valid input files for raw data</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastq1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC508" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastq1</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC509" 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="s" style="color: #d14;">"Input Error: fastq1 file does not exist!</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="LC510" 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="LC511" class="line" lang="python"> <span class="n" style="color: #333;">input_fastq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastq1</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastq2</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC514" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastq2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC515" 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="s" style="color: #d14;">"Input Error: fastq2 file does not exist!</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="LC516" 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="LC517" class="line" lang="python"> <span class="n" style="color: #333;">input_fastq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fastq2</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">input_fastq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if valid input files are provided</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" 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="s" style="color: #d14;">"Input Error: No input file was provided!</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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583
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<pre style="margin: 0;">+<span id="LC583" 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;">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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]):</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" 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="s" style="color: #d14;">"Input Error: Input file does not exist!</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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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</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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586
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<pre style="margin: 0;">+<span id="LC586" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]):</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" 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="s" style="color: #d14;">"Input Error: Input file does not exist!</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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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">infile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span></span>
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">input_fastq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">input_fastq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">infile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</span></span>
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python"></span>
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524
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592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if valid output directory is provided</span></span>
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<pre style="margin: 0;"> <span id="LC593" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out_path</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">@@ -527,26 +595,76 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC595" 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="LC596" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out_path</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If input is an assembly, then use BLAST</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="n" style="color: #333;">finder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ResFinder</span><span class="p">(</span><span class="n" style="color: #333;">db_conf_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_config_file</span><span class="p">,</span> <span class="n" style="color: #333;">databases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">databases</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_path</span><span class="p">,</span> <span class="n" style="color: #333;">notes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">notes_path</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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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"> <span class="n" style="color: #333;">blast_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">blast</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_path</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333;">min_cov</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min_cov</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threshold</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">blast</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">blast_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_results</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blast_run</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">res_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_BLAST</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the input is raw read data, then use KMA</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span><span class="p">(</span><span class="n" style="color: #333;">input_fastq1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">finder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ResFinder</span><span class="p">(</span><span class="n" style="color: #333;">db_conf_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_config_file</span><span class="p">,</span> <span class="n" style="color: #333;">databases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">databases</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_path</span><span class="p">,</span> <span class="n" style="color: #333;">db_path_kma</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">db_path_kma</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="python"> <span class="n" style="color: #333;">notes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">notes_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if input_fastq2 is None, it is ignored by the kma method.</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">kma_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kma</span><span class="p">(</span><span class="n" style="color: #333;">inputfile_1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_fastq1</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile_2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_fastq2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_results</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kma_run</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">res_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ResFinder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TYPE_KMA</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add kma_matrix</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kma_matrix</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="n" style="color: #333;">extra_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-matrix"</span></span>
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<pre style="margin: 0;">+<span id="LC601" 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="LC602" class="line" lang="python"> <span class="n" style="color: #333;">extra_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if valid tmp directory is provided</span></span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC606" 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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC607" 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="s" style="color: #d14;">"Input Error: Tmp dirctory, {}, does not exist!</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="LC608" class="line" lang="python"> <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;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC609" 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="LC610" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</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;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">tmp_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_path</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python"></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_file_format</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">)</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">:</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" 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;">method_path</span><span class="p">:</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="n" style="color: #333;">method_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"kma"</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">find_executable</span><span class="p">(</span><span class="n" style="color: #333;">method_path</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" 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="s" style="color: #d14;">"No valid path to a kma program was provided. Use the -mp "</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="s" style="color: #d14;">"flag to provide the path."</span><span class="p">)</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check the number of files</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" 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;">infile</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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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">infile_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infile</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"> <span class="n" style="color: #333;">infile_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="n" style="color: #333;">infile_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infile</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python"> <span class="n" style="color: #333;">infile_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infile</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" 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="s" style="color: #d14;">"Only 2 input file accepted for raw read data,</span><span class="se" style="color: #d14;">\</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"><span class="s" style="color: #d14;"> if data from more runs is avaliable for the same</span><span class="se" style="color: #d14;">\</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"><span class="s" style="color: #d14;"> sample, please concatinate the reads into two files"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="python"> <span class="n" style="color: #333;">sample_name</span> <span class="o" style="font-weight: 600;">=</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;">basename</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputfile</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="LC637" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"kma"</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="python"> <span class="n" style="color: #333;">finder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ResFinder</span><span class="p">(</span><span class="n" style="color: #333;">db_conf_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_config_file</span><span class="p">,</span> <span class="n" style="color: #333;">databases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">databases</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_path</span><span class="p">,</span> <span class="n" style="color: #333;">db_path_kma</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">db_path</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python"> <span class="n" style="color: #333;">notes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">notes_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if input_fastq2 is None, it is ignored by the kma method.</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="python"> <span class="n" style="color: #333;">kma_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kma</span><span class="p">(</span><span class="n" style="color: #333;">inputfile_1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infile_1</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile_2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infile_2</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span> <span class="n" style="color: #333;">databases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">databases</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">db_path_kma</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">db_path_kma</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">min_cov</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min_cov</span><span class="p">,</span><span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threshold</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="python"> <span class="n" style="color: #333;">kma_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">method_path</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">kma_add_args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python"> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_results</span><span class="p">(</span><span class="n" style="color: #333;">results_method</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kma_run</span><span class="p">,</span><span class="n" style="color: #333;">outdir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC653" 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;">method_path</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="python"> <span class="n" style="color: #333;">method_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"blastn"</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">find_executable</span><span class="p">(</span><span class="n" style="color: #333;">method_path</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" 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="s" style="color: #d14;">"No valid path to a blastn program was provided. Use the "</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python"> <span class="s" style="color: #d14;">"-mp flag to provide the path."</span><span class="p">)</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python"></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Assert that only one fasta file is inputted</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">infile</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="s" style="color: #d14;">"Only one input file accepted for assembled data"</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"> <span class="n" style="color: #333;">infile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infile</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"blast"</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">finder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ResFinder</span><span class="p">(</span><span class="n" style="color: #333;">db_conf_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_config_file</span><span class="p">,</span> <span class="n" style="color: #333;">databases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">databases</span><span class="p">,</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"> <span class="n" style="color: #333;">db_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_path</span><span class="p">,</span> <span class="n" style="color: #333;">notes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">notes_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="n" style="color: #333;">blast_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">blast</span><span class="p">(</span><span class="n" style="color: #333;">inputfile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tmp_dir</span><span class="p">,</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"> <span class="n" style="color: #333;">min_cov</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">min_cov</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threshold</span><span class="p">,</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"> <span class="n" style="color: #333;">blast</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">method_path</span><span class="p">,</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"> <span class="n" style="color: #333;">allowed_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">acq_overlap</span><span class="p">)</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python"> <span class="n" style="color: #333;">finder</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create_results</span><span class="p">(</span><span class="n" style="color: #333;">results_method</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">blast_run</span><span class="p">,</span><span class="n" style="color: #333;">outdir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_path</span><span class="p">)</span></span></pre>
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