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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cct">Debian Med / cct</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74">8c996c30</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-07-20T07:56:31+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.2</pre>
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<h4>27 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b7595d3c080b8ce4e781beed3039039a9f6d424a">
lib/scripts/assign_cogs/test.sh
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<li class="file-stats">
<a href="#5154841788b7a213298c8de7675418b6a81c646b">
lib/scripts/cgview_xml_builder/test_input/R_denitrificans.cogs
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<li class="file-stats">
<a href="#02f017f890838f7f7e624ae465cf173ba7339177">
lib/scripts/convert_vcf_to_features/test.sh
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<a href="#8f6d480e2f0233e20cd50821e5d8905d3056ae1c">
lib/scripts/get_cds/test.sh
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<a href="#89440b309b758d7b8fe5ecd294fec8e791b9f5d2">
lib/scripts/get_orfs/test.sh
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<a href="#7afde62a7e38b40abda1ff0a08dd81bf8d1c64cc">
lib/scripts/local_blast_client/local_blast_client.pl
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<a href="#f36c2e36cff4b3025fde86c438c3f86257aacb2c">
lib/scripts/local_blast_client/test.sh
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<a href="#6bd5d8dbf683a3acd9e36f4d76f729c01e73d5be">
lib/scripts/ncbi_search/README.md
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<a href="#a49286c7e035efc3db26bcffa109062bed45fc5c">
lib/scripts/ncbi_search/ncbi_search.pl
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<a href="#88aa0d5ecc27680f6005434b5a08680fe014d85a">
lib/scripts/ncbi_search/test.sh
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<li class="file-stats">
<a href="#68077feed95de368ae4231d4bd18f87a97ad1dc7">
lib/scripts/sequence_to_multi_fasta/test.sh
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<li class="file-stats">
<a href="#940f8dd45ecfa1b90bd15c6a8e172d65db20be93">
scripts/build_blast_atlas.sh
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<a href="#510a672dfe2348f49b57cd06fa486f9c1cda6509">
scripts/build_blast_atlas_all_vs_all.sh
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<a href="#92b2f4e0d86182d43d04b24efd7028607bddfa3f">
scripts/build_cog_db.sh
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<a href="#7ff4eb941eb6365d5a767be817adbe1bd8e7aed4">
scripts/check_env.sh
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<a href="#bc18b48cfa51ed281404c4b750b92b64f29f535a">
scripts/create_zoomed_maps.sh
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<li class="file-stats">
<a href="#dfcbdbfe68f5bd846eaaae9a4c7e3a19ca7c299c">
scripts/fetch_all_refseq_bacterial_genomes.sh
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<a href="#2d31c3f092433c61481e5c2e79097cd23b2139a0">
scripts/fetch_all_refseq_chloroplast_genomes.sh
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<a href="#08bbb264a5bc8240576f82cf2a891aeb48a2060c">
scripts/fetch_all_refseq_mitochondrial_genomes.sh
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<li class="file-stats">
<a href="#082759aebaa285a43ad2d7fe1b46979cff5a29d1">
scripts/fetch_genome_by_accession.sh
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<a href="#61ee5b50fbfdca800380a0b4d051fc9e8fed277d">
scripts/fetch_refseq_bacterial_genomes_by_name.sh
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<a href="#b190df3d72efbf9c873ac2284cf7cb963267d164">
scripts/process_sample_projects.sh
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<a href="#1e9b61c5b2d0d16d03b6c816a886dfed18dd9f04">
scripts/process_test_projects.sh
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<a href="#bbc190e80f66cb214e9cc6f871ca7814be67cb04">
scripts/redraw_maps.sh
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<a href="#a99676bb9234db7314ede64795c95faa8c944af1">
scripts/remove_long_seqs.sh
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<a href="#907618da0ab3bb98426caa6427f7b53622bc2276">
scripts/remove_short_seqs.sh
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -19,34 +19,33 @@ Pull the Docker image:</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">docker pull pstothard/cgview_comparison_tool</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">Run the Docker image and use <span class="sb" style="color: #d14;">`fetch_genome_by_accession.sh`</span> to download a sequence in GenBank format<span class="idiff left"> (to simplify this and subsequent commands, </span><span class="sb" style="color: #d14;"><span class="idiff">`$CCT`</span></span><span class="idiff right"> is used to store the first part of the command, which runs the Docker image)</span>:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">Run the Docker image and use <span class="sb" style="color: #d14;">`fetch_genome_by_accession.sh`</span> to download a sequence in GenBank format:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="nv" style="color: #008080;">CCT</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"docker run --rm -v </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">:/dir -w /dir pstothard/cgview_comparison_tool"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"><span class="nv" style="color: #008080;">$CCT</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> AC_000022 <span class="nt" style="color: #000080;">-o</span> ./</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">docker run <span class="nt" style="color: #000080;">--rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span>:/dir <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-u</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span>:<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">id</span> <span class="nt" style="color: #000080;">-g</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-w</span> /dir pstothard/cgview_comparison_tool fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> AC_000022 <span class="nt" style="color: #000080;">-o</span> ./</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">Use <span class="sb" style="color: #d14;">`build_blast_atlas.sh`</span> to create a BLAST <span class="idiff left right">A</span>tlas project for the sequence that was downloaded:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">Use <span class="sb" style="color: #d14;">`build_blast_atlas.sh`</span> to create a BLAST <span class="idiff left right">a</span>tlas project for the sequence that was downloaded:</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> build_blast_atlas.sh <span class="nt" style="color: #000080;">-i</span> AC_000022.gbk</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> build_blast_atlas.sh <span class="nt" style="color: #000080;">-i</span> AC_000022.gbk</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown">Download some sequences to be used as "comparison genomes" in the BLAST <span class="idiff left right">A</span>tlas project:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">Download some sequences to be used as "comparison genomes" in the BLAST <span class="idiff left right">a</span>tlas project:</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_046914 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_047196 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_047457 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> AC_000022 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_001326 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_043914 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_046914 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_047196 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_047457 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> AC_000022 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_001326 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_043914 <span class="nt" style="color: #000080;">-o</span> ./AC_000022/comparison_genomes</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown">Generate the CGView maps:</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> build_blast_atlas.sh <span class="nt" style="color: #000080;">-p</span> AC_000022 <span class="nt" style="color: #000080;">-z</span> medium</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> build_blast_atlas.sh <span class="nt" style="color: #000080;">-p</span> AC_000022 <span class="nt" style="color: #000080;">-z</span> medium</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown">Once complete, the maps can be found in the <span class="sb" style="color: #d14;">`AC_000022/maps_for_cds_vs_cds`</span> and <span class="sb" style="color: #d14;">`AC_000022/maps_for_dna_vs_dna`</span> directories on the host system.</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">@@ -56,13 +55,13 @@ There are multiple ways to alter the appearance and contents of a map generated</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown">For example, the following command uses the <span class="p">[</span><span class="nv" style="color: #008080;">--custom option</span><span class="p">](</span><span class="sx" style="color: #d14;">https://paulstothard.github.io/cgview_comparison_tool/customization_keys.html</span><span class="p">)</span> to change several aspects of the map:</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> build_blast_atlas.sh <span class="nt" style="color: #000080;">-p</span> AC_000022 <span class="nt" style="color: #000080;">-x</span> <span class="nt" style="color: #000080;">-z</span> medium <span class="nt" style="color: #000080;">--custom</span> <span class="s2" style="color: #d14;">"title='Example map' global_label=T legend=F use_opacity=F backboneRadius=900 labelFontSize=60 borderColor=white width=3000 height=3000"</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> build_blast_atlas.sh <span class="nt" style="color: #000080;">-p</span> AC_000022 <span class="nt" style="color: #000080;">-x</span> <span class="nt" style="color: #000080;">-z</span> medium <span class="nt" style="color: #000080;">--custom</span> <span class="s2" style="color: #d14;">"title='Example map' global_label=T legend=F use_opacity=F backboneRadius=900 labelFontSize=60 borderColor=white width=3000 height=3000"</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown">This command redraws the maps in SVG format:</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="nv" style="color: #008080;"><span class="idiff left right">$CCT</span></span> redraw_maps.sh <span class="nt" style="color: #000080;">-p</span> AC_000022 <span class="nt" style="color: #000080;">-f</span> svg</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="idiff left">docker run </span><span class="nt" style="color: #000080;"><span class="idiff">--rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-v</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">pwd</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:/dir </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-u</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">:</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-g</span></span><span class="si" style="color: #d14;"><span class="idiff">)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-w</span></span><span class="idiff right"> /dir pstothard/cgview_comparison_tool</span> redraw_maps.sh <span class="nt" style="color: #000080;">-p</span> AC_000022 <span class="nt" style="color: #000080;">-f</span> svg</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>
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68
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown">The SVG maps are added to the <span class="sb" style="color: #d14;">`AC_000022/maps_for_cds_vs_cds`</span> and <span class="sb" style="color: #d14;">`AC_000022/maps_for_dna_vs_dna`</span> directories. Below are the maps generated for the CDS vs CDS comparisons and the DNA vs DNA comparisons, respectively.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,21 +69,6 @@ The SVG maps are added to the `AC_000022/maps_for_cds_vs_cds` and `AC_000022/map</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">CGView map</span><span class="p">](</span><span class="sx" style="color: #d14;">sample1.svg</span><span class="p">)</span></span>
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71
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">CGView map</span><span class="p">](</span><span class="sx" style="color: #d14;">sample2.svg</span><span class="p">)</span></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Tip</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown">When using the CCT Docker image to run commands described in the <span class="p">[</span><span class="nv" style="color: #008080;">CCT documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://paulstothard.github.io/cgview_comparison_tool/index.html</span><span class="p">)</span>, you can store the Docker portion of the command in an environment variable, for example:</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown"><span class="nv" style="color: #008080;">CCT</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"docker run --rm -v </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">:/dir -w /dir pstothard/cgview_comparison_tool"</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown">Then the commands in the CCT documentation can be run by preceding them with the environment variable, for example:</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="markdown"><span class="nv" style="color: #008080;">$CCT</span> fetch_genome_by_accession.sh <span class="nt" style="color: #000080;">-a</span> NC_009787 <span class="nt" style="color: #000080;">-o</span> ./</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="markdown"><span class="nv" style="color: #008080;">$CCT</span> build_blast_atlas.sh <span class="nt" style="color: #000080;">-i</span> NC_009787.gbk</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Downloading and running CCT</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown">To download CCT:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,13 +107,19 @@ export PERL5LIB="$PERL5LIB:${CCT_HOME}/lib/perl_modules"</td>
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123
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown">Test your setup:</span>
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124
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"></span>
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125
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="markdown">check_env.sh</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown">./scripts/check_env.sh</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown">Prepare the COG database:</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown">./scripts/build_cog_db.sh</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"><span class="p">```</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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129
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown">Build some test maps:</span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="markdown">process_test_projects.sh</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="idiff left right">./scripts/</span>process_test_projects.sh</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"><span class="p">```</span></span>
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134
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"></span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown">Refer to the <span class="p">[</span><span class="nv" style="color: #008080;">CCT documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://paulstothard.github.io/cgview_comparison_tool/index.html</span><span class="p">)</span> for information on how to use CCT. The <span class="p">[</span><span class="nv" style="color: #008080;">tutorials</span><span class="p">](</span><span class="sx" style="color: #d14;">https://paulstothard.github.io/cgview_comparison_tool/tutorials.html</span><span class="p">)</span> are a good starting point.</span></pre>
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<li id="b7595d3c080b8ce4e781beed3039039a9f6d424a">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#b7595d3c080b8ce4e781beed3039039a9f6d424a"><strong>lib/scripts/assign_cogs/test.sh</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">@@ -6,29 +6,17 @@ if [ ! -d test_output ]; then</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir </span>test_output</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> db <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir </span>db</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> db/myva <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cp </span>db/myva test_output</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> db/myva.gz <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cp </span>db/myva.gz test_output</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> test_output/myva <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-f</span> db/myva.gz test_output</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gunzip </span>test_output/myva.gz</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> db/whog <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cp </span>db/whog test_output</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> db/whog.gz <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cp </span>db/whog.gz test_output</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> test_output/whog <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-f</span> db/whog.gz test_output</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gunzip </span>test_output/whog.gz</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="idiff left right">formatdb</span> <span class="nt" style="color: #000080;">-p</span> T <span class="nt" style="color: #000080;">-i</span> test_output/myva <span class="nt" style="color: #000080;">-o</span> T</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="idiff left right">FORMATDB</span> <span class="nt" style="color: #000080;">-p</span> T <span class="nt" style="color: #000080;">-i</span> test_output/myva <span class="nt" style="color: #000080;">-o</span> T</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm </span>formatdb.log</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></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">@@ -56,15 +44,16 @@ rm test_output/whog*</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#compare new output to sample output</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nv" style="color: #008080;">new_output</span><span class="o" style="font-weight: 600;">=</span>test_output</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="nv" style="color: #008080;">old_output</span><span class="o" style="font-weight: 600;">=</span>sample_output</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"><span class="nv" style="color: #008080;">new_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span> find <span class="nv" style="color: #008080;">$new_output</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span> <span class="nv" style="color: #008080;">i</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span> i<<span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> i++ <span class="o" style="font-weight: 600;">))</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Comparing </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +e</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$old_file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>diff <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$old_file</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#5154841788b7a213298c8de7675418b6a81c646b"><strong>lib/scripts/cgview_xml_builder/test_input/R_denitrificans.cogs</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,8 +4,8 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">#'start', 'end', and 'strand' information is retrieved.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">seqname source feature start end score strand frame</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">RD0004 R</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">RD0005 Q</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">RD0004 R<span class="idiff left right">Q</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">RD0005 Q<span class="idiff left right">RL</span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">RD0006 R</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">RD0007 R</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">RD0008 L</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">@@ -3789,4 +3789,4 @@ RD4249 A</td>
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3789
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<pre style="margin: 0;"> <span id="LC3789" class="line" lang="plaintext">RD4249 A</span>
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3790
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<pre style="margin: 0;"> <span id="LC3790" class="line" lang="plaintext">RD4250 A</span>
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3791
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<pre style="margin: 0;"> <span id="LC3791" class="line" lang="plaintext">RD4251 A</span>
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<pre style="margin: 0;">-<span id="LC3792" class="line" lang="plaintext">RD4252 R</span></pre>
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<pre style="margin: 0;">+<span id="LC3792" class="line" lang="plaintext">RD4252 R</span></pre>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#02f017f890838f7f7e624ae465cf173ba7339177"><strong>lib/scripts/convert_vcf_to_features/test.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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">@@ -12,15 +12,16 @@ perl convert_vcf_to_features.pl -i test_input/input_multiple_chromosomes.vcf -o</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#compare new output to sample output</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">new_output</span><span class="o" style="font-weight: 600;">=</span>test_output</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">old_output</span><span class="o" style="font-weight: 600;">=</span>sample_output</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">new_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span> find <span class="nv" style="color: #008080;">$new_output</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span> <span class="nv" style="color: #008080;">i</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span> i<<span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> i++ <span class="o" style="font-weight: 600;">))</span><span class="p">;</span></span>
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17
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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19
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Comparing </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +e</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$old_file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>diff <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$old_file</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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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">\ No newline at end of file</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">@@ -13,15 +13,16 @@ perl get_cds.pl -i test_input/prokka_multicontig.gbk -o test_output/prokka_multi</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#compare new output to sample output</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">new_output</span><span class="o" style="font-weight: 600;">=</span>test_output</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">old_output</span><span class="o" style="font-weight: 600;">=</span>sample_output</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nv" style="color: #008080;">new_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span> find <span class="nv" style="color: #008080;">$new_output</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span> <span class="nv" style="color: #008080;">i</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span> i<<span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> i++ <span class="o" style="font-weight: 600;">))</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Comparing </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +e</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$old_file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>diff <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$old_file</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#89440b309b758d7b8fe5ecd294fec8e791b9f5d2"><strong>lib/scripts/get_orfs/test.sh</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">@@ -13,15 +13,16 @@ perl get_orfs.pl -i test_input/prokka_multicontig.gbk -o test_output/prokka_mult</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#compare new output to sample output</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">new_output</span><span class="o" style="font-weight: 600;">=</span>test_output</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">old_output</span><span class="o" style="font-weight: 600;">=</span>sample_output</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nv" style="color: #008080;">new_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span> find <span class="nv" style="color: #008080;">$new_output</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span> <span class="nv" style="color: #008080;">i</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span> i<<span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> i++ <span class="o" style="font-weight: 600;">))</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Comparing </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +e</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$old_file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>diff <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$old_file</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#7afde62a7e38b40abda1ff0a08dd81bf8d1c64cc"><strong>lib/scripts/local_blast_client/local_blast_client.pl</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">@@ -198,7 +198,18 @@ while ( my $sequenceEntry = <SEQFILE> ) {</td>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#-b can be used to specify the number of hits to return when using -m 9. Each hit may consist of one or more HSPs.</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#-b and -v must be set to specify the number of hits to return when using -m 7. Each hit may consist of one or more HSPs.</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$blast_command</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="perl"> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{BLAST_PATH} -p </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{PROGRAM} -d </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{DATABASE} -e </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{EXPECT} -i </span><span class="si" style="color: #d14;">$filename</span><span class="s2" style="color: #d14;"> -b </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{HITLIST_SIZE} -v </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{HITLIST_SIZE} -m </span><span class="si" style="color: #d14;">$format_type</span><span class="s2" style="color: #d14;"> -Q </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{QUERY_GENETIC_CODE} -D </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{DATABASE_GENETIC_CODE} -W </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{WORD_SIZE} -F </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{FILTER}</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="perl"> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{BLAST_PATH} -p </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{PROGRAM} -d </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{DATABASE} -e </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{EXPECT} -i </span><span class="si" style="color: #d14;">$filename</span><span class="s2" style="color: #d14;"> -b </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{HITLIST_SIZE} -v </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{HITLIST_SIZE} -m </span><span class="si" style="color: #d14;">$format_type</span><span class="s2" style="color: #d14;"> -W </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{WORD_SIZE} -F </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{FILTER}</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$settings</span><span class="p">{</span><span class="nv" style="color: #008080;">PROGRAM</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">'</span><span class="s1" style="color: #d14;">blastx</span><span class="p">')</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="perl"> <span class="nv" style="color: #008080;">$blast_command</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;"> -Q </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{QUERY_GENETIC_CODE}</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$settings</span><span class="p">{</span><span class="nv" style="color: #008080;">PROGRAM</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">'</span><span class="s1" style="color: #d14;">tblastn</span><span class="p">')</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="perl"> <span class="nv" style="color: #008080;">$blast_command</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;"> -D </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{DATABASE_GENETIC_CODE}</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$settings</span><span class="p">{</span><span class="nv" style="color: #008080;">PROGRAM</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">'</span><span class="s1" style="color: #d14;">tblastx</span><span class="p">')</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="perl"> <span class="nv" style="color: #008080;">$blast_command</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;"> -Q </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{QUERY_GENETIC_CODE}</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="perl"> <span class="nv" style="color: #008080;">$blast_command</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;"> -D </span><span class="si" style="color: #d14;">$settings</span><span class="s2" style="color: #d14;">{DATABASE_GENETIC_CODE}</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="perl"> <span class="p">}</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="perl"></span>
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203
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span></span>
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="perl"> <span class="p">"</span><span class="s2" style="color: #d14;">Performing BLAST search for sequence number </span><span class="si" style="color: #d14;">$seqCount</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$sequenceTitle</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#f36c2e36cff4b3025fde86c438c3f86257aacb2c"><strong>lib/scripts/local_blast_client/test.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,15 +36,16 @@ rm -rf test_output/formatted_databases</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#compare new output to sample output</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="nv" style="color: #008080;">new_output</span><span class="o" style="font-weight: 600;">=</span>test_output</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="nv" style="color: #008080;">old_output</span><span class="o" style="font-weight: 600;">=</span>sample_output</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="nv" style="color: #008080;">new_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span> find <span class="nv" style="color: #008080;">$new_output</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span> <span class="nv" style="color: #008080;">i</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span> i<<span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> i++ <span class="o" style="font-weight: 600;">))</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Comparing </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +e</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$old_file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>diff <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$old_file</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#6bd5d8dbf683a3acd9e36f4d76f729c01e73d5be"><strong>lib/scripts/ncbi_search/README.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="29" 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">@@ -29,7 +29,7 @@ usage:</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"> perl ncbi_search.pl -help</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">PERFORM NCBI SEARCH<span class="idiff left right">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">PERFORM NCBI SEARCH</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown">usage:</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#a49286c7e035efc3db26bcffa109062bed45fc5c"><strong>lib/scripts/ncbi_search/ncbi_search.pl</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">@@ -255,7 +255,7 @@ usage:</td>
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="perl"></span>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="perl"><span class="s" style="color: #d14;"> perl ncbi_search.pl -help</span></span>
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="perl"></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="perl"><span class="s" style="color: #d14;">PERFORM NCBI SEARCH<span class="idiff left right">:</span></span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="perl"><span class="s" style="color: #d14;">PERFORM NCBI SEARCH</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="perl"><span class="s" style="color: #d14;">usage:</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#88aa0d5ecc27680f6005434b5a08680fe014d85a"><strong>lib/scripts/ncbi_search/test.sh</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">@@ -10,15 +10,16 @@ perl ncbi_search.pl -q 'NC_009925:NC_009934[Accession]' -o test_output -d nuccor</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#compare new output to sample output</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">new_output</span><span class="o" style="font-weight: 600;">=</span>test_output</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nv" style="color: #008080;">old_output</span><span class="o" style="font-weight: 600;">=</span>sample_output</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">new_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span> find <span class="nv" style="color: #008080;">$new_output</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span> <span class="nv" style="color: #008080;">i</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span> i<<span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> i++ <span class="o" style="font-weight: 600;">))</span><span class="p">;</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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17
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Comparing </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +e</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$old_file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>diff <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$old_file</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#68077feed95de368ae4231d4bd18f87a97ad1dc7"><strong>lib/scripts/sequence_to_multi_fasta/test.sh</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">@@ -15,15 +15,16 @@ perl sequence_to_multi_fasta.pl -i test_input/test_seq_multi.fasta -o test_outpu</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#compare new output to sample output</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">new_output</span><span class="o" style="font-weight: 600;">=</span>test_output</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nv" style="color: #008080;">old_output</span><span class="o" style="font-weight: 600;">=</span>sample_output</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">new_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span> find <span class="nv" style="color: #008080;">$new_output</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); foreach(@files) { if (!($_ =~ m/\.svn/)) {print "$_\n";}}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span> <span class="nv" style="color: #008080;">i</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span> i<<span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="p">;</span> i++ <span class="o" style="font-weight: 600;">))</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;"><span class="idiff left">`</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">old_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_output</span><span class="k" style="font-weight: 600;">}</span><span class="si" style="color: #d14;"><span class="idiff left">$(</span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[^\/]+//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Comparing </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">old_file</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +e</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-u</span> <span class="nv" style="color: #008080;">$old_file</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span>diff <span class="nt" style="color: #000080;">-u</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$old_file</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">new_files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"No differences found"</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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28
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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29
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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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">\ No newline at end of file</td>
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<li id="940f8dd45ecfa1b90bd15c6a8e172d65db20be93">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#940f8dd45ecfa1b90bd15c6a8e172d65db20be93"><strong>scripts/build_blast_atlas.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="9" 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">@@ -9,7 +9,7 @@ size=""</td>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">start_at_map</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">start_at_xml</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" 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">@@ -85,7 +85,7 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_filename_without_extension<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"> <span class="nv" style="color: #008080;">basefile</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="shell"> <span class="nv" style="color: #008080;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">basefile</span><span class="p">%.*</span><span class="k" style="font-weight: 600;">}</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$filename</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$filename</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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89
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"></span>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" 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="133" 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">@@ -133,7 +133,7 @@ while [ "$1" != "" ]; do</td>
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133
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="shell"></span>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The CCT_HOME variable must be set</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory."</span></span>
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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="shell"><span class="nv" style="color: #008080;">cct_home</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$CCT_HOME</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="145" 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="145" 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">@@ -145,7 +145,7 @@ elif [ -n "$input" ]; then</td>
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145
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"The input GenBank file '</span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;">' does not exist"</span></span>
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147
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">project_dir</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_filename_without_extension <span class="nv" style="color: #008080;">$input</span><span class="si" style="color: #d14;">)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">project_dir</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_filename_without_extension <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-i' to specify an input sequence file in GenBank format, with .gbk extension or the '-p' option to specify the project directory. For a full list of options use '-h'."</span></span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="227" 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">@@ -227,7 +227,7 @@ if ! $new_project; then</td>
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227
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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228
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="shell"></span>
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229
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$start_at_map</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps_for_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cgview_xml/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span>/maps_for_<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span>/cgview_xml/<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps_for_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cgview_xml/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps_for_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cgview_xml/<span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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231
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Redrawing maps for map type </span><span class="nv" style="color: #008080;">$type</span><span class="s2" style="color: #d14;"> using existing XML."</span></span>
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232
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"> --start_at_map"</span></span>
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<td class="old_line diff-line-num" data-linenumber="233" 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">
233
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Maps drawn to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps_for_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="235" 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="235" 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">@@ -235,7 +235,7 @@ if ! $new_project; then</td>
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235
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"The --start_at_map option was provided but there are no XML files present."</span></span>
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236
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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237
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="shell"><span class="k" style="font-weight: 600;"> elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$start_at_xml</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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238
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/blast/blast_results_local/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="nv" style="color: #008080;">$project_dir</span>/cct_projects/<span class="nv" style="color: #008080;">$type</span>/blast/blast_results_local/<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/blast/blast_results_local/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="nv" style="color: #008080;">$type</span><span class="s2" style="color: #d14;">/blast/blast_results_local/<span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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239
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Redrawing maps for map type </span><span class="nv" style="color: #008080;">$type</span><span class="s2" style="color: #d14;"> using existing BLAST results."</span></span>
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240
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"> --start_at_xml"</span></span>
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241
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Maps drawn to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps_for_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -245,7 +245,7 @@ if ! $new_project; then</td>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="shell"><span class="k" style="font-weight: 600;"> else</span></span>
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Redraw from start</span></span>
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247
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Creating maps for map type </span><span class="nv" style="color: #008080;">$type</span><span class="s2" style="color: #d14;"> in </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps_for_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$command</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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249
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Maps drawn to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps_for_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">type</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="shell"></span>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#510a672dfe2348f49b57cd06fa486f9c1cda6509"><strong>scripts/build_blast_atlas_all_vs_all.sh</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">@@ -11,7 +11,7 @@ start_at_xml=""</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nv" style="color: #008080;">start_at_montage</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nv" style="color: #008080;">columns</span><span class="o" style="font-weight: 600;">=</span>4</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +91,7 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_filename_without_extension<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"> <span class="nv" style="color: #008080;">basefile</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="shell"> <span class="nv" style="color: #008080;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">basefile</span><span class="p">%.*</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$filename</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$filename</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Check for ImageMagick</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">@@ -193,23 +193,22 @@ if (! $new_project) && [ -z "$start_at_montage" ]; then</td>
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Find all the gbk files, sort by accession and for each one create a new cgview_comparison_tool project</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="shell"> <span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="shell"> <span class="nv" style="color: #008080;">files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/comparison_genomes"</span> <span class="nt" style="color: #000080;">-maxdepth</span> 1 <span class="nt" style="color: #000080;">-type</span> f <span class="se" style="color: #d14;">\(</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gbk"</span> <span class="nt" style="color: #000080;">-o</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gb"</span> <span class="se" style="color: #d14;">\)</span> <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); my @sorted = sort {$a =~ m/[AN]C_0*(\d+)/; $a_char = $1; $b =~ m/[AN]C_0*(\d+)/; $b_char = $1; return ($a_char <=> $b_char);} @files; foreach(@sorted) { print "$_\n";}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="shell"> <span class="nv" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < <span class="nv" style="color: #008080;"><span class="idiff left right">$</span>length</span><span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < length<span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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199
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="shell"></span>
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200
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">seqname</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_filename_without_extension <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="shell"> <span class="nv" style="color: #008080;">after</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$i</span>+1</span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="shell"> <span class="nv" style="color: #008080;">after_length</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$length</span>-<span class="nv" style="color: #008080;">$after</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="shell"> <span class="nv" style="color: #008080;">reference_genome</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#the following leaves out the reference genome</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#comparison_genomes=( ${files[@]:0:$i} ${files[@]:$after:$after_length} )</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="shell"> <span class="nv" style="color: #008080;">reference_genome</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="shell"> <span class="nv" style="color: #008080;">comparison_genomes</span><span class="o" style="font-weight: 600;">=(</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[@]</span>:0:<span class="nv" style="color: #008080;">$length</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="shell"> <span class="nv" style="color: #008080;">comparison_genomes</span><span class="o" style="font-weight: 600;">=(</span><span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[@]</span>:0:<span class="nv" style="color: #008080;">$length</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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209
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Generating project for </span><span class="nv" style="color: #008080;">$reference_genome</span><span class="s2" style="color: #d14;"> as the reference genome."</span></span>
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211
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The comparison genomes are:"</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">comparison_genomes</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">comparison_genomes</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Create project and links</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">seqname</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</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">@@ -220,7 +219,7 @@ if (! $new_project) && [ -z "$start_at_montage" ]; then</td>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Create links to comparison genomes</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="shell"> <span class="nv" style="color: #008080;">length_comparison</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">comparison_genomes</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>j <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> j < <span class="nv" style="color: #008080;"><span class="idiff left right">$</span>length_comparison</span><span class="p">;</span> j++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>j <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> j < length_comparison<span class="p">;</span> j++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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224
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">filename_comparison</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">comparison_genomes</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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225
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"../../../comparison_genomes/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">filename_comparison</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">seqname</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/comparison_genomes/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">filename_comparison</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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226
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="242" 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">@@ -243,7 +242,7 @@ if (! $new_project) && [ -z "$start_at_montage" ]; then</td>
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243
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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244
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="shell"></span>
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245
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$start_at_map</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">seqname</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps/cgview_xml/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span>/cct_projects/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">seqname</span><span class="k" style="font-weight: 600;">}</span>/maps/cgview_xml/<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">seqname</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps/cgview_xml/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">project_dir</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">seqname</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/maps/cgview_xml/<span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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247
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#xml present, draw from xml</span></span>
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248
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Redrawing maps for map </span><span class="nv" style="color: #008080;">$seqname</span><span class="s2" style="color: #d14;"> using existing XML."</span></span>
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<td class="old_line diff-line-num" data-linenumber="249" 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">
249
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"> --start_at_map"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" 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="250" 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">@@ -251,7 +250,7 @@ if (! $new_project) && [ -z "$start_at_montage" ]; then</td>
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<td class="old_line diff-line-num" data-linenumber="251" 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">
251
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"The --start_at_map option was provided but there are no XML files present."</span></span>
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252
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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253
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="shell"><span class="k" style="font-weight: 600;"> elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$start_at_xml</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="nv" style="color: #008080;">$seqname</span><span class="s2" style="color: #d14;">/blast/blast_results_local/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="nv" style="color: #008080;">$project_dir</span>/cct_projects/<span class="nv" style="color: #008080;">$seqname</span>/blast/blast_results_local/<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="nv" style="color: #008080;">$seqname</span><span class="s2" style="color: #d14;">/blast/blast_results_local/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-A</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="nv" style="color: #008080;">$seqname</span><span class="s2" style="color: #d14;">/blast/blast_results_local/<span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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255
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#blast results present, build xml and draw</span></span>
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256
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Redrawing maps for map </span><span class="nv" style="color: #008080;">$seqname</span><span class="s2" style="color: #d14;"> using existing BLAST results."</span></span>
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257
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"> --start_at_xml"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="260" 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">@@ -261,7 +260,7 @@ if (! $new_project) && [ -z "$start_at_montage" ]; then</td>
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261
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="shell"><span class="k" style="font-weight: 600;"> else</span></span>
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262
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Redraw from start</span></span>
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263
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Creating maps for map </span><span class="nv" style="color: #008080;">$seqname</span><span class="s2" style="color: #d14;"> in </span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">/cct_projects/</span><span class="nv" style="color: #008080;">$seqname</span><span class="s2" style="color: #d14;">/maps"</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$command</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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265
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="shell"><span class="k" style="font-weight: 600;"> done</span></span>
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267
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" 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="268" 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">@@ -269,12 +268,14 @@ fi</td>
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269
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># COMBINE IMAGES USING IMAGEMAGICK</span></span>
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270
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span> <span class="nv" style="color: #008080;">$new_project</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$start_at_montage</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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271
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># This sorts the files by accession</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="shell"> <span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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272
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="shell"> <span class="nv" style="color: #008080;">png_files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">"</span>/cct_projects <span class="nt" style="color: #000080;">-type</span> f <span class="se" style="color: #d14;">\(</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.png"</span> <span class="se" style="color: #d14;">\)</span> <span class="nt" style="color: #000080;">-print0</span> | perl <span class="nt" style="color: #000080;">-ne</span> <span class="s1" style="color: #d14;">'my @files = split(/\0/, $_); my @sorted = sort {$a =~ m/[A-Z][A-Z]_*0*(\d+)/; $a_char = $1; $b =~ m/[A-Z][A-Z]_*0*(\d+)/; $b_char = $1; return ($a_char <=> $b_char);} @files; foreach(@sorted) { print "$_\n";}'</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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273
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="shell"> <span class="nv" style="color: #008080;">png_length</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">png_files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#for (( i=0; i<$png_length; i++ ));</span></span>
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#do</span></span>
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#convert "${png_files[$i]}" -resize 40% "${png_files[$i]}"</span></span>
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277
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#done</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="shell"> montage <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">png_files</span><span class="p">[@]</span>:0<span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-resize</span> 40% <span class="nt" style="color: #000080;">-tile</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">columns</span><span class="k" style="font-weight: 600;">}</span>x <span class="nt" style="color: #000080;">-geometry</span> 800x800<span class="se" style="color: #d14;">\></span>+2+2 <span class="nt" style="color: #000080;">-background</span> <span class="s2" style="color: #d14;">"#FFFFFF"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">"</span>/montage.png</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="shell"> montage <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">png_files</span><span class="p">[@]</span>:0<span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-resize</span> 40% <span class="nt" style="color: #000080;">-tile</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">columns</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span>x <span class="nt" style="color: #000080;">-geometry</span> 800x800<span class="se" style="color: #d14;">\></span>+2+2 <span class="nt" style="color: #000080;">-background</span> <span class="s2" style="color: #d14;">"#FFFFFF"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">"</span>/montage.png</span>
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279
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Montage drawn to </span><span class="nv" style="color: #008080;">$project_dir</span><span class="s2" style="color: #d14;">/montage.png"</span></span>
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280
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<li id="92b2f4e0d86182d43d04b24efd7028607bddfa3f">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#92b2f4e0d86182d43d04b24efd7028607bddfa3f"><strong>scripts/build_cog_db.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ if [ -z "$CCT_HOME" ]; then</td>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="s2" style="color: #d14;"> For example, add the following to your ~/.bashrc</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;"> or ~/.bash_profile file:</span></span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME="</span>/path/to/cgview_comparison_tool<span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME=</span><span class="se" style="color: #d14;"><span class="idiff left">\</span>"</span><span class="s2" style="color: #d14;">/path/to/cgview_comparison_tool</span><span class="se" style="color: #d14;"><span class="idiff right">\</span>"</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="s2" style="color: #d14;"> After saving reload your ~/.bashrc or ~/.bash_profile file:</span></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="34" 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">@@ -34,7 +34,7 @@ fi</td>
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34
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/cog_db/.complete <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"COG BLAST database already created"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Remove '<span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span>/cog_db/.complete' to create again"</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Remove '</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/cog_db/.complete' to create again"</span></span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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39
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"></span>
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<li id="7ff4eb941eb6365d5a767be817adbe1bd8e7aed4">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#7ff4eb941eb6365d5a767be817adbe1bd8e7aed4"><strong>scripts/check_env.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,7 @@ if [ -z "$CCT_HOME" ]; then</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="s2" style="color: #d14;"> For example, add the following to your ~/.bashrc</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="s2" style="color: #d14;"> or ~/.bash_profile file:</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME="</span>/path/to/cgview_comparison_tool<span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME=</span><span class="se" style="color: #d14;"><span class="idiff left">\</span>"</span><span class="s2" style="color: #d14;">/path/to/cgview_comparison_tool</span><span class="se" style="color: #d14;"><span class="idiff right">\</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="s2" style="color: #d14;"> After saving reload your ~/.bashrc or ~/.bash_profile file:</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"></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">@@ -60,7 +60,7 @@ for j in Util::Configurator Util::LogManager; do</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"><span class="s2" style="color: #d14;"> </span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"><span class="s2" style="color: #d14;"> For example, add the following to your ~/.bashrc or ~/.bash_profile file:</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="shell"><span class="s2" style="color: #d14;"> export PERL5LIB="</span><span class="se" style="color: #d14;">\$</span>PERL5LIB<span class="s2" style="color: #d14;">":"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"/lib/perl_modules</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="s2" style="color: #d14;"> export PERL5LIB=</span><span class="se" style="color: #d14;"><span class="idiff left">\</span>"\$</span><span class="s2" style="color: #d14;">PERL5LIB</span><span class="se" style="color: #d14;"><span class="idiff">\</span>"</span><span class="s2" style="color: #d14;">:</span><span class="se" style="color: #d14;"><span class="idiff">\</span>"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;"><span class="idiff right">\</span>"</span><span class="s2" style="color: #d14;">/lib/perl_modules</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="s2" style="color: #d14;"> After saving reload your ~/.bashrc or ~/.bash_profile file:</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" 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="80" 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">@@ -80,7 +80,7 @@ if ! command -v cgview_comparison_tool.pl &>/dev/null; then</td>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"><span class="s2" style="color: #d14;"> </span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"><span class="s2" style="color: #d14;"> For example, add the following to your ~/.bashrc or ~/.bash_profile file:</span></span>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"><span class="s2" style="color: #d14;"> export PATH="</span><span class="se" style="color: #d14;">\$</span>PATH<span class="s2" style="color: #d14;">":"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"/scripts</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="s2" style="color: #d14;"> export PATH=</span><span class="se" style="color: #d14;"><span class="idiff left">\</span>"\$</span><span class="s2" style="color: #d14;">PATH</span><span class="se" style="color: #d14;"><span class="idiff">\</span>"</span><span class="s2" style="color: #d14;">:</span><span class="se" style="color: #d14;"><span class="idiff">\</span>"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;"><span class="idiff right">\</span>"</span><span class="s2" style="color: #d14;">/scripts</span></span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="s2" style="color: #d14;"> After saving reload your ~/.bashrc or ~/.bash_profile file:</span></span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"></span>
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<li id="bc18b48cfa51ed281404c4b750b92b64f29f535a">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#bc18b48cfa51ed281404c4b750b92b64f29f535a"><strong>scripts/create_zoomed_maps.sh</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">@@ -3,7 +3,7 @@</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">=</span>png</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">mem</span><span class="o" style="font-weight: 600;">=</span>1500m</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</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="shell"></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" 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="43" 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">@@ -43,19 +43,19 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_filename_without_extension<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"> <span class="nv" style="color: #008080;">basefile</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"> <span class="nv" style="color: #008080;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">basefile</span><span class="p">%.*</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$filename</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$filename</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_path_to_maps<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"> <span class="nv" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"> <span class="nv" style="color: #008080;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$file</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'m/(.+)\/cgview_xml\/[^\/]+$/;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $1'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$filename</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$filename</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,22 +116,11 @@ fi</td>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell"><span class="nv" style="color: #008080;">project</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>remove_trailing_slash <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># save and change IFS to avoid problems with filesnames with spaces</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="shell"><span class="nv" style="color: #008080;">OLDIFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$IFS</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#find all XML files in the project</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="shell"><span class="nv" style="color: #008080;">files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="nt" style="color: #000080;">-L</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.xml"</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># restore IFS</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OLDIFS</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="shell"><span class="nv" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < <span class="nv" style="color: #008080;">$length</span><span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">xml_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell">find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.xml"</span> <span class="nt" style="color: #000080;">-type</span> f | <span class="k" style="font-weight: 600;">while </span><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">read</span> <span class="nt" style="color: #000080;">-r</span> xml_file<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Generating zoomed map from the file '</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">'."</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="shell"> <span class="nv" style="color: #008080;">file_no_extension</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_filename_without_extension <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="shell"> <span class="nv" style="color: #008080;">path_to_maps</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_path_to_maps <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="shell"> java <span class="nt" style="color: #000080;">-jar</span> <span class="nt" style="color: #000080;">-Xmx</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">mem</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cct_home</span><span class="s2" style="color: #d14;">"</span>/bin/cgview/cgview.jar <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-c</span> <span class="nv" style="color: #008080;">$center</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$zoom</span> <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$path_to_maps</span><span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="idiff">/</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file_no_extension</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">center</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">zoom</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">.</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"> java <span class="nt" style="color: #000080;">-jar</span> <span class="nt" style="color: #000080;">-Xmx</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">mem</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cct_home</span><span class="s2" style="color: #d14;">"</span>/bin/cgview/cgview.jar <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$center</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;">$zoom</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span> <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$path_to_maps</span><span class="s2" style="color: #d14;"><span class="idiff">/</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file_no_extension</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">center</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">zoom</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span></span>
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136
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"New map drawn to </span><span class="nv" style="color: #008080;">$path_to_maps</span><span class="s2" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file_no_extension</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">center</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">zoom</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">format</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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137
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<li id="dfcbdbfe68f5bd846eaaae9a4c7e3a19ca7c299c">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#dfcbdbfe68f5bd846eaaae9a4c7e3a19ca7c299c"><strong>scripts/fetch_all_refseq_bacterial_genomes.sh</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="37" 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">@@ -37,7 +37,7 @@ function error_exit() {</td>
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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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39
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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41
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"></span>
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43
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="nv" style="color: #008080;">min_length</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" 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="70" 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">@@ -70,7 +70,7 @@ while [ "$1" != "" ]; do</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The CCT_HOME variable must be set</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory."</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="nv" style="color: #008080;">cct_home</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$CCT_HOME</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="92" 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">@@ -92,7 +92,7 @@ if [ -n "$min_length" ]; then</td>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$max_length</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">query</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query</span><span class="s2" style="color: #d14;">" AND </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">min_length</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">:</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">max_length</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">[SLEN]"</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">min_length</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">expr</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$</span>min_length</span> - 1<span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">min_length</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">$(<span class="idiff">(</span></span><span class="idiff"> </span>min_length <span class="o" style="font-weight: 600;">-</span> <span class="m" style="color: #099;">1</span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">))</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="shell"> <span class="nv" style="color: #008080;">query</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query</span><span class="s2" style="color: #d14;">" NOT 1:</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">min_length</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">[SLEN]"</span></span>
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97
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="shell"><span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$max_length</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<li id="2d31c3f092433c61481e5c2e79097cd23b2139a0">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#2d31c3f092433c61481e5c2e79097cd23b2139a0"><strong>scripts/fetch_all_refseq_chloroplast_genomes.sh</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Check for ncbi_search.pl</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" 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">@@ -60,7 +60,7 @@ while [ "$1" != "" ]; do</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"></span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The CCT_HOME variable must be set</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory."</span></span>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="nv" style="color: #008080;">cct_home</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$CCT_HOME</span></span>
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<li id="08bbb264a5bc8240576f82cf2a891aeb48a2060c">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#08bbb264a5bc8240576f82cf2a891aeb48a2060c"><strong>scripts/fetch_all_refseq_mitochondrial_genomes.sh</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="53" 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">@@ -53,7 +53,7 @@ while [ "$1" != "" ]; do</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The CCT_HOME variable must be set</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory."</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="nv" style="color: #008080;">cct_home</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$CCT_HOME</span></span>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#082759aebaa285a43ad2d7fe1b46979cff5a29d1"><strong>scripts/fetch_genome_by_accession.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,7 +33,7 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="59" 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">@@ -59,20 +59,20 @@ while [ "$1" != "" ]; do</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The CCT_HOME variable must be set</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory."</span></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="nv" style="color: #008080;">cct_home</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$CCT_HOME</span></span>
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66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$accession</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$accession</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-a' to specify the accession number of the genome to download. Use '-h' for help."</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$directory</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$directory</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-o' to specify an output directory. Use '-h' for help."</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory"</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" 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">@@ -82,6 +82,6 @@ if [ ! -d "$directory" ]; then</td>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$directory</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell">perl <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cct_home</span><span class="s2" style="color: #d14;"><span class="idiff left">"</span></span>/lib/scripts/ncbi_search/ncbi_search.pl <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$accession</span><span class="s2" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">[</span>ACCESSION] <span class="nt" style="color: #000080;">-d</span> nucleotide <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$directory</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff">/</span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;">$accession</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span>.gbk <span class="nt" style="color: #000080;">-r</span> gbwithparts <span class="nt" style="color: #000080;">-m</span> 1 <span class="nt" style="color: #000080;">-v</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell">perl <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cct_home</span><span class="s2" style="color: #d14;">/lib/scripts/ncbi_search/ncbi_search.pl<span class="idiff left">"</span></span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$accession</span><span class="s2" style="color: #d14;">"</span><span class="s1" style="color: #d14;"><span class="idiff">'</span>[ACCESSION]<span class="idiff">'</span></span> <span class="nt" style="color: #000080;">-d</span> nucleotide <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$directory</span><span class="s2" style="color: #d14;"><span class="idiff">/</span></span><span class="nv" style="color: #008080;">$accession</span><span class="s2" style="color: #d14;">.gbk<span class="idiff right">"</span></span> <span class="nt" style="color: #000080;">-r</span> gbwithparts <span class="nt" style="color: #000080;">-m</span> 1 <span class="nt" style="color: #000080;">-v</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"The record has been saved to </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">directory</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">accession</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.gbk"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#61ee5b50fbfdca800380a0b4d051fc9e8fed277d"><strong>scripts/fetch_refseq_bacterial_genomes_by_name.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,7 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nv" style="color: #008080;">min_length</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,7 +76,7 @@ while [ "$1" != "" ]; do</td>
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"></span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># The CCT_HOME variable must be set</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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80
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory."</span></span>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"><span class="nv" style="color: #008080;">cct_home</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$CCT_HOME</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" 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="102" 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">@@ -102,7 +102,7 @@ if [ -n "$min_length" ]; then</td>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$max_length</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">query</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query</span><span class="s2" style="color: #d14;">" AND </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">min_length</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">:</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">max_length</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">[SLEN]"</span></span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">min_length</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">expr</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$</span>min_length</span> - 1<span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">min_length</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">$(<span class="idiff">(</span></span><span class="idiff"> </span>min_length <span class="o" style="font-weight: 600;">-</span> <span class="m" style="color: #099;">1</span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">))</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="shell"> <span class="nv" style="color: #008080;">query</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query</span><span class="s2" style="color: #d14;">" NOT 1:</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">min_length</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">[SLEN]"</span></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="shell"><span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$max_length</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<li id="b190df3d72efbf9c873ac2284cf7cb963267d164">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#b190df3d72efbf9c873ac2284cf7cb963267d164"><strong>scripts/process_sample_projects.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ if [ -z "$CCT_HOME" ]; then</td>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="s2" style="color: #d14;"> For example, add the following to your ~/.bashrc</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;"> or ~/.bash_profile file:</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME="</span>/path/to/cgview_comparison_tool<span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME=</span><span class="se" style="color: #d14;"><span class="idiff left">\</span>"</span><span class="s2" style="color: #d14;">/path/to/cgview_comparison_tool</span><span class="se" style="color: #d14;"><span class="idiff right">\</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="s2" style="color: #d14;"> After saving reload your ~/.bashrc or ~/.bash_profile file:</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="32" 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">@@ -32,16 +32,18 @@ if [ ! -d "${CCT_HOME}"/test_output ]; then</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/test_output</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="nv" style="color: #008080;">SAMPLE_PROJECTS</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/sample_projects"</span> <span class="nt" style="color: #000080;">-mindepth</span> 1 <span class="nt" style="color: #000080;">-maxdepth</span> 1 <span class="nt" style="color: #000080;">-name</span> <span class="s1" style="color: #d14;">'sample_project_*'</span> <span class="nt" style="color: #000080;">-type</span> d<span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>project <span class="k" style="font-weight: 600;">in</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SAMPLE_PROJECTS</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">p</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Processing project '</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">'"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-R</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/test_output</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>j <span class="k" style="font-weight: 600;">in </span>project_settings_a.conf project_settings_b.conf project_settings_c.conf<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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41
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Processing project '</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">' using configuration '</span><span class="nv" style="color: #008080;">$j</span><span class="s2" style="color: #d14;">'"</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">command</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"perl <span class="idiff left">'</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/scripts/cgview_comparison_tool.pl<span class="idiff">'</span> -g <span class="idiff">'"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff">"</span>/conf/global_settings.conf<span class="idiff">'</span> -p <span class="idiff">'"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff">"</span>/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;"><span class="idiff">'</span> -s <span class="idiff">'"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff">"</span>/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$j</span><span class="s2" style="color: #d14;"><span class="idiff">'</span> -f <span class="idiff">'</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">p</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">j</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_<span class="idiff right">'</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$command</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">command</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"perl </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/scripts/cgview_comparison_tool.pl -g </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/conf/global_settings.conf -p </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;"> -s </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$j</span><span class="s2" style="color: #d14;"> -f </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">p</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">j</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_"</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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46
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Sample project output written to <span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span>/test_output"</span></span></pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Sample project output written to <span class="idiff left">'</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/test_output<span class="idiff right">'</span>"</span></span></pre>
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<li id="1e9b61c5b2d0d16d03b6c816a886dfed18dd9f04">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#1e9b61c5b2d0d16d03b6c816a886dfed18dd9f04"><strong>scripts/process_test_projects.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ if [ -z "$CCT_HOME" ]; then</td>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="s2" style="color: #d14;"> For example, add the following to your ~/.bashrc</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;"> or ~/.bash_profile file:</span></span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME="</span>/path/to/cgview_comparison_tool<span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;"> export CCT_HOME=</span><span class="se" style="color: #d14;"><span class="idiff left">\</span>"</span><span class="s2" style="color: #d14;">/path/to/cgview_comparison_tool</span><span class="se" style="color: #d14;"><span class="idiff right">\</span>"</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="s2" style="color: #d14;"> After saving reload your ~/.bashrc or ~/.bash_profile file:</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="32" 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">@@ -32,16 +32,18 @@ if [ ! -d "${CCT_HOME}"/test_output ]; then</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/test_output</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="nv" style="color: #008080;">TEST_PROJECTS</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/test_projects"</span> <span class="nt" style="color: #000080;">-mindepth</span> 1 <span class="nt" style="color: #000080;">-maxdepth</span> 1 <span class="nt" style="color: #000080;">-name</span> <span class="s1" style="color: #d14;">'test_*'</span> <span class="nt" style="color: #000080;">-type</span> d<span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>project <span class="k" style="font-weight: 600;">in</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TEST_PROJECTS</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">p</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Processing project '</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">'"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-R</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>/test_output</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>j <span class="k" style="font-weight: 600;">in </span>project_settings.conf<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Processing project '</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">' using configuration '</span><span class="nv" style="color: #008080;">$j</span><span class="s2" style="color: #d14;">'"</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">command</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"perl <span class="idiff left">'</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/scripts/cgview_comparison_tool.pl<span class="idiff">'</span> -g <span class="idiff">'"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff">"</span>/conf/global_settings.conf<span class="idiff">'</span> -p <span class="idiff">'"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff">"</span>/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;"><span class="idiff">'</span> -s <span class="idiff">'"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff">"</span>/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$j</span><span class="s2" style="color: #d14;"><span class="idiff">'</span> -f <span class="idiff">'</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">p</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">j</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_<span class="idiff right">'</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$command</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">command</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"perl </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/scripts/cgview_comparison_tool.pl -g </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/conf/global_settings.conf -p </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;"> -s </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/test_output/</span><span class="nv" style="color: #008080;">$p</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$j</span><span class="s2" style="color: #d14;"> -f </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">p</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">j</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_"</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$command</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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44
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test project output written to <span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span>/test_output"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test project output written to <span class="idiff left">'</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CCT_HOME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/test_output<span class="idiff right">'</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#bbc190e80f66cb214e9cc6f871ca7814be67cb04"><strong>scripts/redraw_maps.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">=</span>png</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">mem</span><span class="o" style="font-weight: 600;">=</span>1500m</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -40,19 +40,19 @@ function error_exit() {</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_filename_without_extension<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"> <span class="nv" style="color: #008080;">basefile</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"> <span class="nv" style="color: #008080;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">basefile</span><span class="p">%.*</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$filename</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$filename</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_path_to_maps<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"> <span class="nv" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"> <span class="nv" style="color: #008080;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$file</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'m/(.+)\/cgview_xml\/[^\/]+$/;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $1'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$filename</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$filename</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,7 +85,7 @@ if [ -z "$project" ]; then</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-p' to specify a project. Use '-h' for help."</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="shell"></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$CCT_HOME</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$CCT_HOME</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please set the </span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">CCT_HOME environment variable to the path to the cgview_comparison_tool directory."</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" 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="93" 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">@@ -93,22 +93,17 @@ cct_home=$CCT_HOME</td>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="shell"></span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="shell"><span class="nv" style="color: #008080;">project</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>remove_trailing_slash <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># save and change IFS to avoid problems with filesnames with spaces</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="shell"><span class="nv" style="color: #008080;">OLDIFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$IFS</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="shell"></span>
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100
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#find all XML files in the project</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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101
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="shell"><span class="nv" style="color: #008080;">files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$project</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.xml"</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="shell"></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># restore IFS</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OLDIFS</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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105
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="shell"></span>
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106
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="shell"><span class="nv" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < <span class="nv" style="color: #008080;"><span class="idiff left right">$</span>length</span><span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < length<span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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108
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">xml_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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109
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Generating map from the file '</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">'."</span></span>
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110
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="shell"> <span class="nv" style="color: #008080;">file_no_extension</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_filename_without_extension <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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111
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="shell"> <span class="nv" style="color: #008080;">path_to_maps</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_path_to_maps <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="shell"> java <span class="nt" style="color: #000080;">-jar</span> <span class="nt" style="color: #000080;">-Xmx</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">mem</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cct_home</span><span class="s2" style="color: #d14;">"</span>/bin/cgview/cgview.jar <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$path_to_maps</span><span class="s2" style="color: #d14;">"</span>/<span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file_no_extension</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>.<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"> java <span class="nt" style="color: #000080;">-jar</span> <span class="nt" style="color: #000080;">-Xmx</span><span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">mem</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cct_home</span><span class="s2" style="color: #d14;">"</span>/bin/cgview/cgview.jar <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$xml_file</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$path_to_maps</span><span class="s2" style="color: #d14;">"</span>/<span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file_no_extension</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span>.<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$format</span><span class="s2" style="color: #d14;">"</span></span>
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113
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Map drawn to </span><span class="nv" style="color: #008080;">$path_to_maps</span><span class="s2" style="color: #d14;">/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">file_no_extension</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">format</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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114
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#a99676bb9234db7314ede64795c95faa8c944af1"><strong>scripts/remove_long_seqs.sh</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="34" 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">@@ -34,13 +34,13 @@ function error_exit() {</td>
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34
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_sequence_length<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"> <span class="nv" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"> <span class="nv" style="color: #008080;">seq_length</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n</span> 1 <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$file</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'m/(\d+)\sbp/;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $1'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$seq_length</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$seq_length</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,7 +69,7 @@ if [ -z "$input" ]; then</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-i' to specify an input directory of GenBank files with .gbk extensions. Use '-h' for help."</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$max_length</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$max_length</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-l' to specify a maximum sequence length to keep. Use '-h' for help."</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"></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">@@ -77,23 +77,18 @@ cct_home=$CCT_HOME</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"><span class="nv" style="color: #008080;">input</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>remove_trailing_slash <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># save and change IFS to avoid problems with filesnames with spaces</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="shell"><span class="nv" style="color: #008080;">OLDIFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$IFS</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#find all GenBank files in the directory</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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85
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"><span class="nv" style="color: #008080;">files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-maxdepth</span> 1 <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gbk"</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="shell"></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># restore IFS</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OLDIFS</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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89
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"></span>
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90
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="nv" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="shell"><span class="nb" style="color: #0086b3;"><span class="idiff left">echo</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$length</span></span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < <span class="nv" style="color: #008080;"><span class="idiff left right">$</span>length</span><span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < length<span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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93
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">gbk_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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94
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="shell"> <span class="nv" style="color: #008080;">seq_length</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_sequence_length <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$gbk_file</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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95
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$seq_length</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$seq_length</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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97
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Unable to determine length of sequence '</span><span class="nv" style="color: #008080;">$gbk_file</span><span class="s2" style="color: #d14;">'"</span></span>
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98
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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99
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="shell"></span>
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<li id="907618da0ab3bb98426caa6427f7b53622bc2276">
<a href="https://salsa.debian.org/med-team/cct/-/commit/8c996c301859f25f037fd3ccbe1870a29cdaaf74#907618da0ab3bb98426caa6427f7b53622bc2276"><strong>scripts/remove_short_seqs.sh</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash -e</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span><span class="si" style="color: #d14;">)</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>usage<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"usage: remove_short_seqs.sh [[-i input] [-l length] | [-h]]"</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">@@ -37,13 +37,13 @@ function error_exit() {</td>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>remove_trailing_slash<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"> <span class="nv" style="color: #008080;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"> <span class="nv" style="color: #008080;">new_string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$string</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/\/+$//;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $_'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$new_string</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$new_string</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>get_sequence_length<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"> <span class="nv" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"> <span class="nv" style="color: #008080;">seq_length</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n</span> 1 <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$file</span><span class="s2" style="color: #d14;">"</span> | perl <span class="nt" style="color: #000080;">-nl</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'m/(\d+)\sbp/;'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'print $1'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$seq_length</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$seq_length</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</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">@@ -68,11 +68,11 @@ while [ "$1" != "" ]; do</td>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$input</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-i' to specify an input directory of GenBank files with .gbk extensions. Use '-h' for help."</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$min_length</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$min_length</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Please use '-l' to specify a minimum sequence length to keep. Use '-h' for help."</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,22 +80,17 @@ cct_home=$CCT_HOME</td>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"><span class="nv" style="color: #008080;">input</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>remove_trailing_slash <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># save and change IFS to avoid problems with filesnames with spaces</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="shell"><span class="nv" style="color: #008080;">OLDIFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$IFS</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#find all GenBank files in the directory</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">$'</span><span class="se" style="color: #d14;">\n</span><span class="s1" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="nv" style="color: #008080;">files</span><span class="o" style="font-weight: 600;">=(</span><span class="si" style="color: #d14;">$(</span>find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$input</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-maxdepth</span> 1 <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gbk"</span><span class="si" style="color: #d14;">)</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="shell"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># restore IFS</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="shell"><span class="nv" style="color: #008080;">IFS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OLDIFS</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>IFS</span>
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92
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="shell"></span>
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93
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="shell"><span class="nv" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${#</span><span class="nv" style="color: #008080;">files</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < <span class="nv" style="color: #008080;"><span class="idiff left right">$</span>length</span><span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"><span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span>i <span class="o" style="font-weight: 600;">=</span> 0<span class="p">;</span> i < length<span class="p">;</span> i++<span class="o" style="font-weight: 600;">))</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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95
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">gbk_file</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">files</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="k" style="font-weight: 600;">}</span></span>
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96
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="shell"> <span class="nv" style="color: #008080;">seq_length</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>get_sequence_length <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$gbk_file</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">)</span></span>
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97
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$seq_length</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;">$seq_length</span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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99
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>error_exit <span class="s2" style="color: #d14;">"Unable to determine length of sequence '</span><span class="nv" style="color: #008080;">$gbk_file</span><span class="s2" style="color: #d14;">'"</span></span>
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100
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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101
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="shell"></span>
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