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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/igdiscover">Debian Med / igdiscover</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/igdiscover/-/commit/11f77113b8b9318c00567647d641057588b8e501">11f77113</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-02T14:31:20+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.12.3</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#75132b09bc7fd9f5dea89dee58ea9a22eae4b9e9">
src/igdiscover/Snakefile
</a>
</li>
<li class="file-stats">
<a href="#a5a09087f75e40ea7564bb0d420e8b10f6bafe7d">
src/igdiscover/cli/clonoquery.py
</a>
</li>
<li class="file-stats">
<a href="#e9d6343d326202eab04dc5220bb8f7fc875664d0">
src/igdiscover/cli/clonotypes.py
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<li class="file-stats">
<a href="#06c40582f46cbc98ba550a19989a93a286dcd40e">
tests/test_commands.py
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<li class="file-stats">
<a href="#570726290219a04b926b9aa2c02fe1ba4204124a">
tests/utils.py
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<h4>Changes:</h4>
<li id="75132b09bc7fd9f5dea89dee58ea9a22eae4b9e9">
<a href="https://salsa.debian.org/med-team/igdiscover/-/commit/11f77113b8b9318c00567647d641057588b8e501#75132b09bc7fd9f5dea89dee58ea9a22eae4b9e9"><strong>src/igdiscover/Snakefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="330" 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="330" 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">@@ -330,7 +330,12 @@ else:</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="plaintext"> input: fastaq='reads/3-forward-primer-trimmed.{ext}.gz'</span>
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<td class="diff-line-num old_line" data-linenumber="331" 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">
331
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="plaintext"> resources: time=1</span>
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="plaintext"> run:</span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext"> relative_symlink(input.fastaq, output.fastaq, force=True)</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> if config.forward_primers:</span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"> # The target is marked as temp().</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"> # To avoid a dangling symlink, use a hardlink.</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext"> os.link(input.fastaq, output.fastaq)</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"> else:</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"> relative_symlink(input.fastaq, output.fastaq, force=True)</span>
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334
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="plaintext">rule trimmed_fasta_stats:</span>
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<li id="a5a09087f75e40ea7564bb0d420e8b10f6bafe7d">
<a href="https://salsa.debian.org/med-team/igdiscover/-/commit/11f77113b8b9318c00567647d641057588b8e501#a5a09087f75e40ea7564bb0d420e8b10f6bafe7d"><strong>src/igdiscover/cli/clonoquery.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="30" 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">@@ -30,7 +30,6 @@ def add_arguments(parser):</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--minimum-count'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-c'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;"> <span id="LC32" 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;">'Discard all rows with count less than N. Default: %(default)s'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--v-shm-threshold'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'V SHM threshold for _mindiffrate computations'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--cdr3-core'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">slice_arg</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'START:END'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'START:END defines the non-junction region of CDR3 '</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">@@ -93,7 +92,7 @@ def collect(querytable, reftable, mismatches, cdr3_core_slice, cdr3_column):</td>
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93
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">([</span><span class="n" style="color: #333;">query_row</span><span class="p">],</span> <span class="n" style="color: #333;">reftable</span><span class="p">.</span><span class="n" style="color: #333;">head</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="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</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="LC96" class="line" lang="python"> <span class="n" style="color: #333;">similar_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vjlen_group</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">),</span> <span class="p">:]</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">similar_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vjlen_group</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">),</span> <span class="p">:]<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">copy</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">query_rows</span><span class="p">,</span> <span class="n" style="color: #333;">similar_group</span><span class="p">)</span></span>
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98
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>
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99
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Yield result tuples for all the queries that have not been found</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" 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="137" 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">@@ -138,13 +137,11 @@ def main(args):</td>
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138
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">summary_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" 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="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">Print h</span>eader</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">H</span>eader</span></span>
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142
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">reftable</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Do the actual work</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">query_rows</span><span class="p">,</span> <span class="n" style="color: #333;">result_table</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">collect</span><span class="p">(</span><span class="n" style="color: #333;">querytable</span><span class="p">,</span> <span class="n" style="color: #333;">reftable</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatches</span><span class="p">,</span></span>
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146
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cdr3_core</span><span class="p">,</span> <span class="n" style="color: #333;">cdr3_column</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">result_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">augment_group</span><span class="p">(</span><span class="n" style="color: #333;">result_table</span><span class="p">,</span> <span class="n" style="color: #333;">v_shm_threshold</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">v_shm_threshold</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC145" 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;">query_rows</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span></span>
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149
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">summary_file</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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">query_row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">query_rows</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/igdiscover/-/commit/11f77113b8b9318c00567647d641057588b8e501#e9d6343d326202eab04dc5220bb8f7fc875664d0"><strong>src/igdiscover/cli/clonotypes.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">@@ -234,9 +234,8 @@ def augment_group(table, v_shm_threshold=5, suffix='_mindiffrate'):</td>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">column</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">columns</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;">root_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">root</span><span class="p">[</span><span class="n" style="color: #333;">column</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;">table</span><span class="p">[</span><span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left right">[</span></span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">column</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">suffix</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">table</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">column</span></span><span class="p"><span class="idiff">].</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">apply</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="p"><span class="idiff right">:</span></span></span>
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">edit_distance</span><span class="p">(</span><span class="n" style="color: #333;">root_seq</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">maxdiff</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="mf" style="color: #099;">0.2</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;">root_seq</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;">root_seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">100.</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="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">column</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span></span></pre>
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<a href="https://salsa.debian.org/med-team/igdiscover/-/commit/11f77113b8b9318c00567647d641057588b8e501#06c40582f46cbc98ba550a19989a93a286dcd40e"><strong>tests/test_commands.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">contextlib</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">igdiscover.__main__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span></span>
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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;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datapath</span><span class="p">,</span> <span class="n" style="color: #333;">resultpath</span><span class="p">,</span> <span class="n" style="color: #333;">files_equal</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datapath</span><span class="p">,</span> <span class="n" style="color: #333;">resultpath</span><span class="p">,</span> <span class="n" style="color: #333;">files_equal</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">convert_fastq_to_fasta</span></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">igdiscover.cli.init</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">run_init</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">igdiscover.cli.config</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_configuration</span><span class="p">,</span> <span class="n" style="color: #333;">modify_configuration</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">igdiscover.cli.run</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">run_snakemake</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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">@@ -154,6 +156,27 @@ def test_primers(pipeline_dir):</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">run_snakemake</span><span class="p">(</span><span class="n" style="color: #333;">dryrun</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># TODO slow</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_only_forward_primer</span><span class="p">(</span><span class="n" style="color: #333;">pipeline_dir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># issue #107 (broken symlink)</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">pipeline_dir</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;">modify_configuration</span><span class="p">(</span><span class="n" style="color: #333;">settings</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">"forward_primers"</span><span class="p">,</span> <span class="s" style="color: #d14;">"['CGTGA']"</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="c1" style="color: #998; font-style: italic;"># Create some dummy files so we don’t need to run irrelevant steps of the pipeline</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;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="s" style="color: #d14;">"reads"</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;">r</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"2-merged.fastq.gz"</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;">f</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="k" style="font-weight: 600;">pass</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;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="s" style="color: #d14;">"stats"</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="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" 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;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"merging-successful"</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;">f</span><span class="p">:</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</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;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"reads.json"</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;">f</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{"total": 0}'</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="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;">s</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"trimmed.json"</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;">f</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;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{"trimmed": 0}'</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="n" style="color: #333;">run_snakemake</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"reads/sequences.fasta.gz"</span><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>
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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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157
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_flash</span><span class="p">(</span><span class="n" style="color: #333;">pipeline_dir</span><span class="p">):</span></span>
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158
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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;"># Test using FLASH and parsing its log output</span></span>
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159
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">pipeline_dir</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" 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="241" 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">@@ -218,11 +241,3 @@ def test_fasta_input(has_filtered_tab, tmp_path):</td>
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218
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">directory</span><span class="p">):</span></span>
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219
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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;">modify_configuration</span><span class="p">([(</span><span class="s" style="color: #d14;">"barcode_length_3prime"</span><span class="p">,</span> <span class="s" style="color: #d14;">"21"</span><span class="p">)])</span></span>
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220
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">run_snakemake</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"stats/reads.json"</span><span class="p">])</span></span></pre>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">convert_fastq_to_fasta</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">inf</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta</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;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">inf</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;">outf</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/igdiscover/-/commit/11f77113b8b9318c00567647d641057588b8e501#570726290219a04b926b9aa2c02fe1ba4204124a"><strong>tests/utils.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,8 @@ import subprocess</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">contextmanager</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">contextmanager</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">capture_stdout</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">@@ -25,3 +27,9 @@ def resultpath(path):</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">files_equal</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">([</span><span class="s" style="color: #d14;">'diff'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-u'</span><span class="p">,</span> <span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">])</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="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">convert_fastq_to_fasta</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">inf</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fasta</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;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">inf</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">outf</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span></pre>
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