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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/cct">Debian Med / cct</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cct/-/commit/81fe02761caad0d43edeae51bdd5974213ddb90f">81fe0276</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-10-19T16:14:21-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Address BLAST usage errors as of BLAST+ 2.10.
debian/patches/conditionalize_blast_-Q_-D.patch (new): Supply the
legacy blastall command's -Q and -D flags only in BLAST variants that
involve translating queries and subjects respectively. (tblastx
notably translates both.)
NB: The use of -v $settings{HITLIST_SIZE} in conjunction with the
supplied $format_type value (7 or 9) results in the warning
Warning: [tblastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output
Actually substituting -max_target_seqs would require bypassing the
legacy blastall wrapper, which isn't entirely straightforward in this
instance due to the need to convert a variable format string to modern
options. (Also, this script technically only knows the path to
blastall, though that shouldn't be a concern in practice on Debian.)
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#db92f62a0924537d681cc0ace09f8f30bdcb5870">
<span class="new-file">
+
debian/patches/conditionalize_blast_-Q_-D.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/cct/-/commit/81fe02761caad0d43edeae51bdd5974213ddb90f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">cct (20170919+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Depends: ncbi-blast+-legacy, imagemagick | graphicsmagick, liberror-perl,</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> libwww-perl</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</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="8" 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">@@ -7,11 +8,15 @@ cct (20170919+dfsg-2) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Remove trailing whitespace in debian/copyright (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> TODO: Either restrict the test suite to those tests that are compatible</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> with current blast or hope for answers to</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> https://lists.debian.org/debian-med/2020/10/msg00103.html</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 16 Oct 2020 10:15:34 +0200</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> [ Aaron M. Ucko ]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * debian/patches/conditionalize_blast_-Q_-D.patch (new): Address BLAST</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> usage errors as of BLAST+ 2.10 by supplying the legacy blastall</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> command's -Q and -D flags only in BLAST variants that involve</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> translating queries and subjects respectively. (tblastx notably</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> translates both.)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Mon, 19 Oct 2020 16:14:20 -0400</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">cct (20170919+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<li id="db92f62a0924537d681cc0ace09f8f30bdcb5870">
<a href="https://salsa.debian.org/med-team/cct/-/commit/81fe02761caad0d43edeae51bdd5974213ddb90f#db92f62a0924537d681cc0ace09f8f30bdcb5870"><strong>debian/patches/conditionalize_blast_-Q_-D.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Aaron M. Ucko <ucko@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 19 Oct 2020 16:14:20 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Address BLAST usage errors as of BLAST+ 2.10.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Supply the legacy blastall command's -Q and -D flags only in BLAST</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">variants that involve translating queries and subjects respectively.</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">(tblastx</span> notably translates both.)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">NB: The use of -v $settings{HITLIST_SIZE} in conjunction with the</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">supplied $format_type value (7 or 9) results in the warning</span></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"> Warning: [tblastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output</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">Actually substituting -max_target_seqs would require bypassing the</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">legacy blastall wrapper, which isn't entirely straightforward in this</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">instance due to the need to convert a variable format string to modern</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">options. (Also, this script technically only knows the path to</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">blastall, though that shouldn't be a concern in practice on Debian.)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff">--- a/lib/scripts/local_blast_client/local_blast_client.pl</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/scripts/local_blast_client/local_blast_client.pl</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -254,7 +254,16 @@</span> while ( my $sequenceEntry = <SEQFILE> )</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #-b can be used to specify the number of hits to return when using -m 9. Each hit may consist of one or more HSPs.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> #-b and -v must be set to specify the number of hits to return when using -m 7. Each hit may consist of one or more HSPs.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> my $blast_command</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- = "$settings{BLAST_PATH} -p $settings{PROGRAM} -d $settings{DATABASE} -e $settings{EXPECT} -i $filename -b $settings{HITLIST_SIZE} -v $settings{HITLIST_SIZE} -m $format_type -Q $settings{QUERY_GENETIC_CODE} -D $settings{DATABASE_GENETIC_CODE} -W $settings{WORD_SIZE} -F $settings{FILTER}";</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ = "$settings{BLAST_PATH} -p $settings{PROGRAM} -d $settings{DATABASE} -e $settings{EXPECT} -i $filename -b $settings{HITLIST_SIZE} -v $settings{HITLIST_SIZE} -m $format_type -W $settings{WORD_SIZE} -F $settings{FILTER}";</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ($settings{ALIGN_TYPE} eq 'TRANSLATED') {</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ($settings{INPUTTYPE} eq 'DNA') {</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $blast_command .= "-Q $settings{QUERY_GENETIC_CODE}";</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Not elsif; tblastx notably accepts both.</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ($settings{ENTREZ_DB} eq 'nucleotide') {</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $blast_command .= "-D $settings{DATABASE_GENETIC_CODE}";</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> print</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> "Performing BLAST search for sequence number $seqCount ($sequenceTitle).\n";</span></pre>
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<a href="https://salsa.debian.org/med-team/cct/-/commit/81fe02761caad0d43edeae51bdd5974213ddb90f#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">@@ -2,3 +2,4 @@ cgview_path.patch</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">testscripts.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_cgview_path.patch</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># debug.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">conditionalize_blast_-Q_-D.patch</span></pre>
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