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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/t-coffee">Debian Med / t-coffee</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/-/commit/f29b730018844fa1ad92fb4653a94ddb3b2e631f">f29b7300</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-04-16T16:00:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove un-needed patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/-/commit/349ea6cd9a3cec163ef5d157ad111e3fbceaa24d">349ea6cd</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-04-16T16:00:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt tests with new version
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#8b7aede91f63a56963c57c21edec1407bbb19ab9">
<span class="deleted-file">
−
debian/patches/fix_tempfile_name_sharing.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="8b7aede91f63a56963c57c21edec1407bbb19ab9">
<a href="https://salsa.debian.org/med-team/t-coffee/-/compare/c2aee3eedc05bcc2dc3ac06cea52fa3e34305cca...349ea6cd9a3cec163ef5d157ad111e3fbceaa24d#8b7aede91f63a56963c57c21edec1407bbb19ab9"><strong>debian/patches/fix_tempfile_name_sharing.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Liubov Chuprikova <chuprikovalv@gmail.com> </span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/917143</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Sun, 03 Feb 2019 23:42:41 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Description: Delete static for tempfile names so that </span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">different processes do not use the same file.</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/t_coffee_source/util_lib/reformat.c</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/t_coffee_source/util_lib/reformat.c</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -6201,6 +6201,8 @@</span> Alignment * read_gotoh_aln ( char *fname</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vfree(tmp_name1);</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vfree(tmp_name2);</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> vfclose (fp);</span></pre>
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<a href="https://salsa.debian.org/med-team/t-coffee/-/compare/c2aee3eedc05bcc2dc3ac06cea52fa3e34305cca...349ea6cd9a3cec163ef5d157ad111e3fbceaa24d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -6,5 +6,4 @@ set_proper_dir_permissions.patch</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">mayhem.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">stable-linking-inputs.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">clustalw2.patch</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">fix_tempfile_name_sharing.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">verbose_build</span></pre>
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<a href="https://salsa.debian.org/med-team/t-coffee/-/compare/c2aee3eedc05bcc2dc3ac06cea52fa3e34305cca...349ea6cd9a3cec163ef5d157ad111e3fbceaa24d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -15,26 +15,25 @@ find . -name "*.gz" -exec gunzip \{\} \;</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;"># Make sure HOME is set in environment (see bug #909530)</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: #008080;">$PWD</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">t_coffee sample_seq1.fasta </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell">t_coffee sample_seq1.fasta <span class="nt" style="color: #000080;">-mode</span> quickaln </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">t_coffee sample_seq1.fasta <span class="nt" style="color: #000080;">-mode</span> quickaln <span class="nt" style="color: #000080;">-ndiag</span><span class="o" style="font-weight: 600;">=</span>10 </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-aln</span><span class="o" style="font-weight: 600;">=</span>sproteases_small.cw_aln, sproteases_small.muscle, sproteases_small.tc_aln <span class="nt" style="color: #000080;">-outfile</span><span class="o" style="font-weight: 600;">=</span>combined_aln.aln </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-infile</span><span class="o" style="font-weight: 600;">=</span>sproteases_small.aln <span class="nt" style="color: #000080;">-special_mode</span><span class="o" style="font-weight: 600;">=</span>evaluate </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sproteases_small.aln <span class="nt" style="color: #000080;">-output</span> fasta_aln <span class="o" style="font-weight: 600;">></span> sproteases_small.fasta_aln </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sproteases_small.aln <span class="nt" style="color: #000080;">-output</span> msf <span class="o" style="font-weight: 600;">></span> sproteases_small.msf </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sproteases_small.aln <span class="nt" style="color: #000080;">-output</span> fasta_seq <span class="o" style="font-weight: 600;">></span> sproteases_small.fasta </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sproteases_small.aln <span class="nt" style="color: #000080;">-action</span> +lower <span class="nt" style="color: #000080;">-output</span> clustalw </span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +upper +edit_residue hmgb_chite 10 lower </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +upper +3evaluate idmat +lower <span class="s1" style="color: #d14;">''</span> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sproteases_large.fasta <span class="nt" style="color: #000080;">-output</span> code_name <span class="o" style="font-weight: 600;">></span> sproteases_large.code_name </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-code</span> sproteases_large.code_name <span class="nt" style="color: #000080;">-in</span> sproteases_large.fasta <span class="o" style="font-weight: 600;">></span>sproteases_large.coded.fasta </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-decode</span> sproteases_large.code_name <span class="nt" style="color: #000080;">-in</span> sproteases_large.coded.fasta </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +3convert a0 <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> colored.html </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +color_residue hmgb_chite 10 1 <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> color.html </span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +3evaluate pam250mt <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> color.html </span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +3evaluate boxshade <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> color.html </span>
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36
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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC36" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_aln6.aln <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>clustalw_aln <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>cache.aln <span class="nt" style="color: #000080;">-action</span> +convert <span class="s1" style="color: #d14;">'Aa1'</span> <span class="s1" style="color: #d14;">'.--'</span> +convert <span class="s1" style="color: #d14;">'#0'</span> </span>
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37
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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC37" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_aln6.aln <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>fasta_seq <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>cache.seq <span class="nt" style="color: #000080;">-action</span> +convert <span class="s1" style="color: #d14;">'Aa1'</span> <span class="s1" style="color: #d14;">'.--'</span> +convert <span class="s1" style="color: #d14;">'#0'</span> </span>
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38
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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC38" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_aln6.aln <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>fasta_seq <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>cache <span class="nt" style="color: #000080;">-action</span> +convert <span class="s1" style="color: #d14;">'Aa1'</span> <span class="s1" style="color: #d14;">'.--'</span> </span>
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39
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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC39" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_aln6.aln <span class="nt" style="color: #000080;">-struc_in</span><span class="o" style="font-weight: 600;">=</span>sample_aln6.cache <span class="nt" style="color: #000080;">-struc_in_f</span> number_fasta <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>color_html <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>x.html </span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"></span></pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">t_coffee sample_rnaseq1.fasta</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">t_coffee sample_rnaseq1.fasta <span class="nt" style="color: #000080;">-mode</span> quickaln</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">t_coffee sample_rnaseq1.fasta <span class="nt" style="color: #000080;">-mode</span> quickaln <span class="nt" style="color: #000080;">-ndiag</span><span class="o" style="font-weight: 600;">=</span>10</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">t_coffee proteases_small.fasta <span class="nt" style="color: #000080;">-aln</span> g0.aln g5.aln g10.aln g15.aln <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>clustalw,html</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-infile</span><span class="o" style="font-weight: 600;">=</span>sample_aln1.aln <span class="nt" style="color: #000080;">-lib</span><span class="o" style="font-weight: 600;">=</span>sample_aln1.tc_lib <span class="nt" style="color: #000080;">-special_mode</span><span class="o" style="font-weight: 600;">=</span>evaluate</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> proteases_small.aln <span class="nt" style="color: #000080;">-output</span> fasta_aln <span class="o" style="font-weight: 600;">></span> proteases_small.fasta_aln</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> proteases_small.aln <span class="nt" style="color: #000080;">-output</span> msf <span class="o" style="font-weight: 600;">></span> proteases_small.msf</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> proteases_small.aln <span class="nt" style="color: #000080;">-output</span> fasta_seq <span class="o" style="font-weight: 600;">></span> proteases_small.fasta</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> proteases_small.aln <span class="nt" style="color: #000080;">-action</span> +lower <span class="nt" style="color: #000080;">-output</span> clustalw</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +upper +edit_residue hmgb_chite 10 lower</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +upper +3evaluate idmat +lower <span class="s1" style="color: #d14;">''</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> proteases_large.fasta <span class="nt" style="color: #000080;">-output</span> code_name <span class="o" style="font-weight: 600;">></span> proteases_large.code_name</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-code</span> proteases_large.code_name <span class="nt" style="color: #000080;">-in</span> proteases_large.fasta <span class="o" style="font-weight: 600;">></span>proteases_large.coded.fasta</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-decode</span> proteases_large.code_name <span class="nt" style="color: #000080;">-in</span> proteases_large.coded.fasta</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +3convert a0 <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> colored.html</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +color_residue hmgb_chite 10 1 <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> color.html</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +3evaluate pam250mt <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> color.html</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span> sample_aln1.aln <span class="nt" style="color: #000080;">-in3</span> sample_aln1.aln <span class="nt" style="color: #000080;">-action</span> +3evaluate boxshade <span class="nt" style="color: #000080;">-output</span> color_html <span class="o" style="font-weight: 600;">></span> color.html</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_dnaseq2.aln <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>clustalw_aln <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>cache.aln <span class="nt" style="color: #000080;">-action</span> +convert <span class="s1" style="color: #d14;">'Aa1'</span> <span class="s1" style="color: #d14;">'.--'</span> +convert <span class="s1" style="color: #d14;">'#0'</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_dnaseq2.aln <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>fasta_seq <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>cache.seq <span class="nt" style="color: #000080;">-action</span> +convert <span class="s1" style="color: #d14;">'Aa1'</span> <span class="s1" style="color: #d14;">'.--'</span> +convert <span class="s1" style="color: #d14;">'#0'</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_dnaseq2.aln <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>fasta_seq <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>cache <span class="nt" style="color: #000080;">-action</span> +convert <span class="s1" style="color: #d14;">'Aa1'</span> <span class="s1" style="color: #d14;">'.--'</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">t_coffee <span class="nt" style="color: #000080;">-other_pg</span> seq_reformat <span class="nt" style="color: #000080;">-in</span><span class="o" style="font-weight: 600;">=</span>sample_dnaseq2.aln <span class="nt" style="color: #000080;">-struc_in</span><span class="o" style="font-weight: 600;">=</span>sample_dnaseq2.cache <span class="nt" style="color: #000080;">-struc_in_f</span> number_fasta <span class="nt" style="color: #000080;">-output</span><span class="o" style="font-weight: 600;">=</span>color_html <span class="nt" style="color: #000080;">-out</span><span class="o" style="font-weight: 600;">=</span>x.html</span></pre>
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