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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/busco">Debian Med / busco</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/0dba43385fbd72234a904d33da5092a9d5c7afe9">0dba4338</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-08T18:31:32+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.1.4</pre>
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<h4>4 changed files:</h4>
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<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#200a2d1cfa2fb65158ca0f851c48c1054f174e7a">
src/busco/BuscoTools.py
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<a href="#ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88">
src/busco/_version.py
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<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/busco/-/commit/0dba43385fbd72234a904d33da5092a9d5c7afe9#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">4.1.4</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Fix Augustus parsing bug</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">4.1.3</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">- Issue #296 fixed</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">- Issue #305 fixed</span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/busco/-/commit/0dba43385fbd72234a904d33da5092a9d5c7afe9#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**BUSCOv4 - Benchmarking sets of Universal Single-Copy Orthologs.**</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">######Note: v4.1.3 is the latest stable release. To access v5.beta clone this repository and checkout the v5 branch with `git checkout v5.beta`</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">######Note: v4.1.4 is the latest stable release. To access v5.beta clone this repository and checkout the v5 branch with `git checkout v5.beta`</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">######Note: A critical bug was discovered to have been introduced in v4.1.3. Any analysis on eukaryote genomes done with this version should be repeated with v4.1.4.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">For full documentation please consult the user guide: https://busco.ezlab.org/busco_userguide.html</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<li id="200a2d1cfa2fb65158ca0f851c48c1054f174e7a">
<a href="https://salsa.debian.org/med-team/busco/-/commit/0dba43385fbd72234a904d33da5092a9d5c7afe9#200a2d1cfa2fb65158ca0f851c48c1054f174e7a"><strong>src/busco/BuscoTools.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="512" 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="512" 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">@@ -512,7 +512,8 @@ class HMMERRunner(BaseRunner):</td>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">input_sequences</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">input_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">f</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">input_sequences</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">).</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="n" style="color: #333;">busco_id</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;">for</span> <span class="n" style="color: #333;">seq_filename</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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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">output_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">seq_filename</span><span class="p">).</span><span class="n" style="color: #333;">rpartition</span><span class="p">(</span><span class="s" style="color: #d14;">".faa"</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="s" style="color: #d14;">".out"</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">filename_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">seq_filename</span><span class="p">).</span><span class="n" style="color: #333;">rpartition</span><span class="p">(</span><span class="s" style="color: #d14;">".faa"</span><span class="p">)</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">output_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename_parts</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="s" style="color: #d14;">".out"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename_parts</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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516
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">busco_id</span><span class="p">,</span> <span class="n" style="color: #333;">seq_filename</span><span class="p">,</span> <span class="n" style="color: #333;">output_filename</span></span>
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"></span>
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</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">@@ -1931,38 +1932,50 @@ class AugustusRunner(BaseRunner):</td>
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="python"></span>
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1932
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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1933
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1934
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<pre style="margin: 0;"> <span id="LC1934" class="line" lang="python"></span>
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1934
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<pre style="margin: 0;">-<span id="LC1934" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">aa_sequence_section</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"# end gene"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"]"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">):</span></span>
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1935
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<pre style="margin: 0;">-<span id="LC1935" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_section</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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1936
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<pre style="margin: 0;">-<span id="LC1936" class="line" lang="python"> <span class="n" style="color: #333;">completed_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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1937
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<pre style="margin: 0;">-<span id="LC1937" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_id</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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1938
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<pre style="margin: 0;">-<span id="LC1938" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">)</span></span>
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1939
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<pre style="margin: 0;">-<span id="LC1939" class="line" lang="python"> <span class="n" style="color: #333;">nt_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">nt_sequence_parts</span><span class="p">)</span></span>
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1940
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<pre style="margin: 0;">-<span id="LC1940" class="line" lang="python"> <span class="n" style="color: #333;">seq_record_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">aa_sequence</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>
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1941
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<pre style="margin: 0;">-<span id="LC1941" class="line" lang="python"> <span class="n" style="color: #333;">seq_record_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">nt_sequence</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>
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1942
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<pre style="margin: 0;">-<span id="LC1942" class="line" lang="python"> <span class="n" style="color: #333;">sequences_aa</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record_aa</span><span class="p">)</span></span>
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1943
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<pre style="margin: 0;">-<span id="LC1943" class="line" lang="python"> <span class="n" style="color: #333;">sequences_nt</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record_nt</span><span class="p">)</span></span>
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1944
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<pre style="margin: 0;">-<span id="LC1944" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1945
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<pre style="margin: 0;">-<span id="LC1945" class="line" lang="python"> <span class="n" style="color: #333;">nt_sequence_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1946
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<pre style="margin: 0;">-<span id="LC1946" class="line" lang="python"> <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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1947
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<pre style="margin: 0;">-<span id="LC1947" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1948
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<pre style="margin: 0;">-<span id="LC1948" class="line" lang="python"></span>
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1949
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<pre style="margin: 0;">-<span id="LC1949" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">aa_sequence_section</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"# sequence of block"</span><span class="p">):</span></span>
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1950
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<pre style="margin: 0;">-<span id="LC1950" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_section</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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1951
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<pre style="margin: 0;">-<span id="LC1951" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1952
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<pre style="margin: 0;">-<span id="LC1952" class="line" lang="python"></span>
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1953
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1935
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<pre style="margin: 0;"> <span id="LC1935" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">aa_sequence_section</span><span class="p">:</span></span>
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1954
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<pre style="margin: 0;">-<span id="LC1954" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"# "</span><span class="p">).</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"]"</span><span class="p">)</span></span>
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1955
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<pre style="margin: 0;">-<span id="LC1955" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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1956
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<pre style="margin: 0;">-<span id="LC1956" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1936
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<pre style="margin: 0;">+<span id="LC1936" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"]"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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1937
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<pre style="margin: 0;">+<span id="LC1937" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"# "</span><span class="p">).</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"]"</span><span class="p">)</span></span>
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1938
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<pre style="margin: 0;">+<span id="LC1938" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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1939
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<pre style="margin: 0;">+<span id="LC1939" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_section</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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1940
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<pre style="margin: 0;">+<span id="LC1940" class="line" lang="python"> <span class="n" style="color: #333;">completed_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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1941
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<pre style="margin: 0;">+<span id="LC1941" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_id</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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1942
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<pre style="margin: 0;">+<span id="LC1942" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">)</span></span>
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1943
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<pre style="margin: 0;">+<span id="LC1943" class="line" lang="python"> <span class="n" style="color: #333;">nt_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">nt_sequence_parts</span><span class="p">)</span></span>
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1944
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<pre style="margin: 0;">+<span id="LC1944" class="line" lang="python"> <span class="n" style="color: #333;">seq_record_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">aa_sequence</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>
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1945
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<pre style="margin: 0;">+<span id="LC1945" class="line" lang="python"> <span class="n" style="color: #333;">seq_record_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">nt_sequence</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>
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1946
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<pre style="margin: 0;">+<span id="LC1946" class="line" lang="python"> <span class="n" style="color: #333;">sequences_aa</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record_aa</span><span class="p">)</span></span>
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1947
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<pre style="margin: 0;">+<span id="LC1947" class="line" lang="python"> <span class="n" style="color: #333;">sequences_nt</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record_nt</span><span class="p">)</span></span>
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1948
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<pre style="margin: 0;">+<span id="LC1948" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1949
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<pre style="margin: 0;">+<span id="LC1949" class="line" lang="python"> <span class="n" style="color: #333;">nt_sequence_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1950
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<pre style="margin: 0;">+<span id="LC1950" class="line" lang="python"> <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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1951
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<pre style="margin: 0;">+<span id="LC1951" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1952
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<pre style="margin: 0;">+<span id="LC1952" class="line" lang="python"></span>
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1953
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<pre style="margin: 0;">+<span id="LC1953" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1954
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<pre style="margin: 0;">+<span id="LC1954" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"# "</span><span class="p">).</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"]"</span><span class="p">)</span></span>
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1955
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<pre style="margin: 0;">+<span id="LC1955" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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1956
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<pre style="margin: 0;">+<span id="LC1956" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1957
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1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="python"></span>
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1958
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1958
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<pre style="margin: 0;"> <span id="LC1958" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"# protein"</span><span class="p">):</span></span>
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1959
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1959
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<pre style="margin: 0;"> <span id="LC1959" class="line" lang="python"> <span class="n" style="color: #333;">nt_sequence_section</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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1960
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1960
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<pre style="margin: 0;"> <span id="LC1960" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_section</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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1961
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1961
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<pre style="margin: 0;"> <span id="LC1961" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"]"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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1962
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<pre style="margin: 0;">+<span id="LC1962" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"]"</span><span class="p">).</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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1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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1962
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1964
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<pre style="margin: 0;"> <span id="LC1964" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_section</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
</pre>
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1963
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1965
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<pre style="margin: 0;"> <span id="LC1965" class="line" lang="python"> <span class="n" style="color: #333;">completed_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
</pre>
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1964
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<pre style="margin: 0;">-<span id="LC1964" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"]"</span><span class="p">).</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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1965
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<pre style="margin: 0;">-<span id="LC1965" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1966" 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">
1966
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<pre style="margin: 0;">+<span id="LC1966" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gene_id</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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<td class="diff-line-num new new_line" data-linenumber="1967" 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">
1967
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<pre style="margin: 0;">+<span id="LC1967" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">)</span></span>
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1968
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<pre style="margin: 0;">+<span id="LC1968" class="line" lang="python"> <span class="n" style="color: #333;">nt_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">nt_sequence_parts</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1969" 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">
1969
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<pre style="margin: 0;">+<span id="LC1969" class="line" lang="python"> <span class="n" style="color: #333;">seq_record_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">aa_sequence</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1970" 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">
1970
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<pre style="margin: 0;">+<span id="LC1970" class="line" lang="python"> <span class="n" style="color: #333;">seq_record_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="n" style="color: #333;">nt_sequence</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gene_id</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1971" 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">
1971
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<pre style="margin: 0;">+<span id="LC1971" class="line" lang="python"> <span class="n" style="color: #333;">sequences_aa</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record_aa</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1972" 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">
1972
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<pre style="margin: 0;">+<span id="LC1972" class="line" lang="python"> <span class="n" style="color: #333;">sequences_nt</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record_nt</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1973" 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">
1973
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<pre style="margin: 0;">+<span id="LC1973" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1974" 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">
1974
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<pre style="margin: 0;">+<span id="LC1974" class="line" lang="python"> <span class="n" style="color: #333;">nt_sequence_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1975" 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">
1975
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<pre style="margin: 0;">+<span id="LC1975" class="line" lang="python"> <span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1976" 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">
1976
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<pre style="margin: 0;">+<span id="LC1976" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1977" 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">
1977
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<pre style="margin: 0;">+<span id="LC1977" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"]"</span><span class="p">).</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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1978
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<pre style="margin: 0;">+<span id="LC1978" class="line" lang="python"> <span class="n" style="color: #333;">aa_sequence_parts</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
</pre>
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1966
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1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1967
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<td class="diff-line-num new_line" data-linenumber="1980" 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">
1980
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<pre style="margin: 0;"> <span id="LC1980" class="line" lang="python"></span>
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1968
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1981
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<pre style="margin: 0;"> <span id="LC1981" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nt_sequence_section</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/commit/0dba43385fbd72234a904d33da5092a9d5c7afe9#ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88"><strong>src/busco/_version.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">@@ -6,4 +6,4 @@ Copyright (c) 2016-2020, Evgeny Zdobnov (ez@ezlab.org)</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"4.1.<span class="idiff left right">3</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"4.1.<span class="idiff left right">4</span>"</span></span></pre>
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