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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-tools6">Debian Med / ncbi-tools6</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/d446096240ea9d4d7873deaea4b09cbb210bbf37">d4460962</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-04-10T16:44:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest: continue to improve tests by checking its output content
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
debian/source/include-binaries
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</li>
<li class="file-stats">
<a href="#6fb62b17bee1d130ce422b1f1ae6caa289c7007a">
<span class="new-file">
+
debian/tests/test-data/dsRNA_viruses.gene_info.gz
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</li>
<li class="file-stats">
<a href="#d5a28aca73e03038ef6d2b2b036f5a2c218066f3">
debian/tests/test-data/trnascan-se_sample.output
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/d446096240ea9d4d7873deaea4b09cbb210bbf37#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -14,13 +14,14 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr></td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: public_domain</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Files: debian/tests/test-data/nc0225.aso.gz</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> debian/tests/test-data/dsRNA_viruses.<span class="idiff left right">ags.gz</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> debian/tests/test-data/dsRNA_viruses.<span class="idiff left right">*</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Copyright: 1996-2018 NCBI </span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Comment: </span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> To dowload the files use:</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0225.aso.gz</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Viruses/dsRNA_viruses.gene_info.gz</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Files: debian/tests/test-data/trnascan-se_sample.output</span>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Comment:</span>
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<li id="d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/d446096240ea9d4d7873deaea4b09cbb210bbf37#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">debian/tests/test-data/nc0225.aso.gz</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/tests/test-data/dsRNA_viruses.ags.gz</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/test-data/dsRNA_viruses.gene_info.gz</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/d446096240ea9d4d7873deaea4b09cbb210bbf37#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="58" 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">@@ -58,16 +58,83 @@ echo '---asn2gb test---'</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="nv" style="color: teal;">gbk</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"^LOCUS "</span> nc0225.gbk<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$genes</span> <span class="nt" style="color: navy;">-eq</span> <span class="nv" style="color: teal;">$gbk</span> <span class="o" style="font-weight: 600;">]</span></span>
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60
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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;">##################################################################</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2xml test---'</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell">/usr/bin/asn2xml <span class="nt" style="color: navy;">-i</span> nc0225.text <span class="nt" style="color: navy;">-b</span> F <span class="nt" style="color: navy;">-o</span> nc0225.xml</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225.xml <span class="o" 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="nv" style="color: teal;">dna_xml</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'<Seq-inst_mol value="dna"/>'</span> nc0225.xml<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="nv" style="color: teal;">rna_xml</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'<Seq-inst_mol value="rna"/>'</span> nc0225.xml<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="nv" style="color: teal;">proteins_xml</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'<Seq-inst_mol value="aa"/>'</span> nc0225.xml<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$genes</span> <span class="nt" style="color: navy;">-eq</span> <span class="k" style="font-weight: 600;">$(</span>expr <span class="nv" style="color: teal;">$dna_xml</span> + <span class="nv" style="color: teal;">$rna_xml</span><span class="k" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">]</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$proteins</span> <span class="nt" style="color: navy;">-eq</span> <span class="nv" style="color: teal;">$proteins_xml</span> <span class="o" style="font-weight: 600;">]</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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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---cleanasn test---'</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell">/usr/bin/cleanasn <span class="nt" style="color: navy;">-a</span> t <span class="nt" style="color: navy;">-D</span> t <span class="nt" style="color: navy;">-i</span> nc0225.text <span class="nt" style="color: navy;">-o</span> nc0225_cleaned.text</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225_cleaned.text <span class="o" style="font-weight: 600;">]</span></span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="nv" style="color: teal;">titles</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">" title </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span> nc0225.text<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"><span class="nv" style="color: teal;">titles_to_clean</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-A</span> 1 <span class="s2" style="color: #d14;">" descr {$"</span> nc0225.text | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">" title </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"><span class="nv" style="color: teal;">titles_left</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">" title </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span> nc0225_cleaned.text<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">$(</span>expr <span class="nv" style="color: teal;">$titles</span> - <span class="nv" style="color: teal;">$titles_to_clean</span><span class="k" style="font-weight: 600;">)</span> <span class="nt" style="color: navy;">-eq</span> <span class="nv" style="color: teal;">$titles_left</span> <span class="o" style="font-weight: 600;">]</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</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;">echo</span> <span class="s1" style="color: #d14;">'---gene2xml test---'</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell">/usr/bin/gene2xml <span class="nt" style="color: navy;">-b</span> <span class="nt" style="color: navy;">-i</span> dsRNA_viruses.ags <span class="nt" style="color: navy;">-o</span> dsRNA_viruses.xgs</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> dsRNA_viruses.xgs <span class="o" style="font-weight: 600;">]</span></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;"># The content in dsRNA_viruses.gene_info mirrors the content in dsRNA_viruses.ags</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: teal;">first_id</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span>awk <span class="s1" style="color: #d14;">'NR==2{print $1}'</span> dsRNA_viruses.gene_info<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"><span class="nv" style="color: teal;">last_id</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span>awk <span class="s1" style="color: #d14;">'END{print $1}'</span> dsRNA_viruses.gene_info<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># check the beginning of the output</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="nv" style="color: teal;">start_in</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"^</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">first_id</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> dsRNA_viruses.gene_info<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"><span class="nv" style="color: teal;">start_out</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"<Object-id_id></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">first_id</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"></Object-id_id>"</span> dsRNA_viruses.xgs<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$start_in</span> <span class="nt" style="color: navy;">-eq</span> <span class="nv" style="color: teal;">$start_out</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#check the ending of the output</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"><span class="nv" style="color: teal;">end_in</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"^</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">last_id</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> dsRNA_viruses.gene_info<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"><span class="nv" style="color: teal;">end_out</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"<Object-id_id></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">last_id</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"></Object-id_id>"</span> dsRNA_viruses.xgs<span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$end_in</span> <span class="nt" style="color: navy;">-eq</span> <span class="nv" style="color: teal;">$end_out</span> <span class="o" style="font-weight: 600;">]</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"></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="LC100" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># _insdseqget_ and _idfetch_ testing requires internet connection.</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Comment the lines below to skip the testing.</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'GI:'</span> nc0225.gbk | head | sed <span class="s1" style="color: #d14;">'s/.*GI://'</span> <span class="o" style="font-weight: 600;">></span> GIs.txt</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell">check_GI<span class="o" style="font-weight: 600;">()</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"> <span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">read </span>GI<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$GI</span> <span class="nv" style="color: teal;">$1</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;">done</span> < <span class="nv" style="color: teal;">$2</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---insdseqget test---'</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell">/usr/bin/insdseqget <span class="nt" style="color: navy;">-i</span> GIs.txt <span class="o" style="font-weight: 600;">></span> insdset.xml</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> insdset.xml <span class="o" style="font-weight: 600;">]</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell">check_GI insdset.xml GIs.txt</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---idfetch test---'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell">/usr/bin/idfetch <span class="nt" style="color: navy;">-G</span> GIs.txt <span class="nt" style="color: navy;">-o</span> idfetch.text</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> idfetch.text <span class="o" style="font-weight: 600;">]</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell">check_GI idfetch.text GIs.txt</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---vecscreen test---'</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell">/usr/bin/vecscreen <span class="nt" style="color: navy;">-f</span> 3 < nc0225.fna <span class="o" style="font-weight: 600;">></span> vecscreen.output</span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> vecscreen.output <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"><span class="nv" style="color: teal;">last_in</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">">"</span> nc0225.fna | tail <span class="nt" style="color: navy;">-1</span> | sed <span class="s1" style="color: #d14;">'s/>//'</span> | sed <span class="s1" style="color: #d14;">'s/ .*//'</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 new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"><span class="nv" style="color: teal;">last_out</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">">"</span> vecscreen.output | tail <span class="nt" style="color: navy;">-1</span> | sed <span class="s1" style="color: #d14;">'s/>Vector //'</span> | sed <span class="s1" style="color: #d14;">'s/ .*//'</span><span class="k" style="font-weight: 600;">)</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$last_in</span><span class="o" style="font-weight: 600;">==</span><span class="nv" style="color: teal;">$last_out</span> <span class="o" style="font-weight: 600;">]</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"></span>
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61
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="shell"></span>
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62
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<td class="diff-line-num 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">
133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2idx test---'</span></span>
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63
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<td class="diff-line-num new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="shell">/usr/bin/asn2idx <span class="nt" style="color: navy;">-p</span> <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-x</span> .text < nc0225.text</span>
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64
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225.idx <span class="o" style="font-weight: 600;">]</span></span>
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65
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<td class="diff-line-num new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> master.idx <span class="o" style="font-weight: 600;">]</span></span>
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66
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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="shell"></span>
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67
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<td class="diff-line-num new_line old" data-linenumber="138" 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="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2xml test---'</span></span>
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68
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<td class="diff-line-num new_line old" data-linenumber="138" 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="LC68" class="line" lang="shell">/usr/bin/asn2xml <span class="nt" style="color: navy;">-i</span> nc0225.text <span class="nt" style="color: navy;">-b</span> F <span class="nt" style="color: navy;">-o</span> nc0225.xml</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225.xml <span class="o" style="font-weight: 600;">]</span></span>
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70
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<td class="diff-line-num new_line old" data-linenumber="138" 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="LC70" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
71
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<td class="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asndisc test---'</span></span>
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<td class="diff-line-num old_line" data-linenumber="72" 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">
72
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<td class="diff-line-num new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="shell">/usr/bin/asndisc <span class="nt" style="color: navy;">-i</span> nc0225.text <span class="nt" style="color: navy;">-a</span> t <span class="nt" style="color: navy;">-o</span> nc0225.disc</span>
</pre>
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73
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<td class="diff-line-num new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225.disc <span class="o" style="font-weight: 600;">]</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">@@ -84,28 +151,10 @@ echo '---asntool test---'</td>
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84
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="shell">/usr/bin/asntool <span class="nt" style="color: navy;">-m</span> asnpub.all <span class="nt" style="color: navy;">-v</span> medline.ent <span class="nt" style="color: navy;">-p</span> asntool.output</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> asntool.output <span class="o" style="font-weight: 600;">]</span></span>
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86
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153
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<pre style="margin: 0;"> <span id="LC153" 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="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---cleanasn test---'</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="shell">/usr/bin/cleanasn <span class="nt" style="color: navy;">-a</span> t <span class="nt" style="color: navy;">-D</span> t <span class="nt" style="color: navy;">-i</span> nc0225.text <span class="nt" style="color: navy;">-o</span> nc0225_cleaned.text</span>
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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 class="nt" style="color: navy;">-s</span> nc0225_cleaned.text <span class="o" style="font-weight: 600;">]</span></span>
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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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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---debruijn test---'</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="shell">/usr/bin/debruijn <span class="nt" style="color: navy;">-a</span> ncbistdaa <span class="nt" style="color: navy;">-n</span> 4 <span class="o" style="font-weight: 600;">></span> debruijn.output</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> debruijn.output <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---gene2xml test---'</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="shell">/usr/bin/gene2xml <span class="nt" style="color: navy;">-b</span> <span class="nt" style="color: navy;">-i</span> dsRNA_viruses.ags <span class="nt" style="color: navy;">-o</span> dsRNA_viruses.xgs</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> dsRNA_viruses.xgs <span class="o" style="font-weight: 600;">]</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># _insdseqget_ and _idfetch_ testing requires internet connection.</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Comment the lines below to skip the testing.</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'GI:'</span> nc0225.gbk | head | sed <span class="s1" style="color: #d14;">'s/.*GI://'</span> <span class="o" style="font-weight: 600;">></span> GIs.txt</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---insdseqget test---'</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="shell">/usr/bin/insdseqget <span class="nt" style="color: navy;">-n</span> <span class="nt" style="color: navy;">-i</span> GIs.txt <span class="o" style="font-weight: 600;">></span> insdset.xml</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> insdset.xml <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---idfetch test---'</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="shell">/usr/bin/idfetch <span class="nt" style="color: navy;">-G</span> GIs.txt <span class="nt" style="color: navy;">-t</span> 2 <span class="nt" style="color: navy;">-o</span> idfetch.aso</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> idfetch.aso <span class="o" style="font-weight: 600;">]</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="shell"></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---tbl2asn test---'</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="shell">/usr/bin/tbl2asn <span class="nt" style="color: navy;">-t</span> Sc_16.sbt <span class="nt" style="color: navy;">-i</span> Sc_16.fsa</span>
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111
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> Sc_16.sqn <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -117,7 +166,3 @@ echo '---trna2tbl test---'</td>
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117
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="shell">/usr/bin/trna2tbl < trnascan-se_sample.output <span class="o" style="font-weight: 600;">></span> trna2tbl.output</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> trna2tbl.output <span class="o" style="font-weight: 600;">]</span></span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---vecscreen test---'</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="shell">/usr/bin/vecscreen <span class="nt" style="color: navy;">-f</span> 3 < nc0225.fna <span class="o" style="font-weight: 600;">></span> vecscreen.output</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> vecscreen.output <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/d446096240ea9d4d7873deaea4b09cbb210bbf37#6fb62b17bee1d130ce422b1f1ae6caa289c7007a"><strong>debian/tests/test-data/dsRNA_viruses.gene_info.gz</strong></a>
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<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/d446096240ea9d4d7873deaea4b09cbb210bbf37#d5a28aca73e03038ef6d2b2b036f5a2c218066f3"><strong>debian/tests/test-data/trnascan-se_sample.output</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"></span>
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2
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">tRNAscan-SE v.2.0 (December 2017) - scan sequences for transfer RNAs</span>
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3
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Copyright (C) 2017 Patricia Chan and Todd Lowe</span>
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4
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> University of California Santa Cruz</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="6" 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">@@ -7,7 +6,7 @@ Freely distributed under the GNU General Public License (GPLv3)</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Sequence file(s) to search: /usr/share/doc/trnascan-se/examples/Example1.fa</span>
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9
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Search Mode: Eukaryotic</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Results written to: t<span class="idiff left right">estrun.o</span>ut</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Results written to: t<span class="idiff left right">rnascan-se_sample.outp</span>ut</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
11
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<td class="diff-line-num new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Output format: Tabular</span>
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<td class="diff-line-num 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">
12
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<td class="diff-line-num new_line" data-linenumber="11" 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">
11
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Searching with: Infernal First Pass->Infernal</span>
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<td class="diff-line-num old_line" data-linenumber="13" 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">
13
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Isotype-specific model scan: Yes</span>
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