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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl">Debian Med / libbio-db-ncbihelper-perl</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f">620c9401</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-01-04T12:44:49+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.7.6</pre>
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<h4>16 changed files:</h4>
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<li class="file-stats">
<a href="#8aa57de6dce6ee1c35c6aba7426503281876b258">
Changes
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<li class="file-stats">
<a href="#4a6da301633ce81aa21cac64ffb95d87c6894995">
META.json
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<li class="file-stats">
<a href="#3b7f8f92275828b66b32cb6c6aeb61e73c1d7587">
META.yml
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<li class="file-stats">
<a href="#a6a4139b0f32af1594c237ebe008acaf8217f505">
Makefile.PL
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<li class="file-stats">
<a href="#384adeead2ae33537082bc3db4b10a27220e76ca">
dist.ini
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<li class="file-stats">
<a href="#88a8729aee4b852e491f1f6e67064c25fdc872ec">
lib/Bio/DB/EntrezGene.pm
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<a href="#a84412d8551a98a5524a93620ede1b428d2395bd">
lib/Bio/DB/GenBank.pm
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<li class="file-stats">
<a href="#aff401a99f6558c2d03e3f3b80e58ab886212a13">
lib/Bio/DB/GenPept.pm
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<li class="file-stats">
<a href="#002bf5ec2dc04ef6165f2361f313f45e3b0ac7ca">
lib/Bio/DB/NCBIHelper.pm
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<li class="file-stats">
<a href="#08f0cedb845978af21d4ee7737d5850f52129211">
lib/Bio/DB/Query/GenBank.pm
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<a href="#f85d1f5169454d0f079cda8a369165345bd7c6d9">
lib/Bio/DB/Taxonomy/entrez.pm
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<a href="#75a796bca1acd6cefec2fb423331df522d057729">
t/EntrezGene.t
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<a href="#96ec5a5ce3dd8358677c3c1f0d8596336500eb52">
t/GenBank.t
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<a href="#e9878a920144a470d96a07badd950289de96555d">
t/GenPept.t
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<li class="file-stats">
<a href="#ec7c119f53c9107709a5005c78ceaa939da98aaa">
t/Query-Genbank.t
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<a href="#48ff9b4488f6ca56e79f22bc26b9048a7458c76b">
t/Taxonomy.t
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<h4>Changes:</h4>
<li id="8aa57de6dce6ee1c35c6aba7426503281876b258">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#8aa57de6dce6ee1c35c6aba7426503281876b258"><strong>Changes</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Summary of important user-visible changes for Bio-DB-NCBIHelper</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"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext">1.7.6 2019-12-07 16:11:22-06:00 America/Chicago</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Requires Bio::DB::WebDBSeqI v1.7.7</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">1.7.5 2019-11-29 16:55:33-06:00 America/Chicago</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Explicitly add Bio::SeqIO::entrezgene and LWP::Protocol::https as dependencies</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Actually get '-email' to work which requires overriding get_seq_stream</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Fix remaining delay settings in tests which are causing issues during peak</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> NCBI times</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">1.7.4 2019-03-10 21:29:52-05:00 America/Chicago</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Switch away from Bio::Root::Test</span>
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Add '-email' parameter, which allows lower delay interval at NCBI (currently</span>
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<li id="4a6da301633ce81aa21cac64ffb95d87c6894995">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#4a6da301633ce81aa21cac64ffb95d87c6894995"><strong>META.json</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" 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">@@ -30,18 +30,20 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"runtime"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"requires"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::DB::Query::WebQuery"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"<span class="idiff left right">0</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::DB::Query::WebQuery"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"<span class="idiff left right">v1.7.7</span>"</span><span class="p">,</span></span>
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34
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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::DB::Taxonomy"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::DB::WebDBSeqI"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="36" 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">
36
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<td class="diff-line-num new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::Root::IO"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
37
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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::Root::Root"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="38" 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">
38
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<td class="diff-line-num new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::SeqIO"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::SeqIO::entrezgene"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
39
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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::Taxon"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
40
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<td class="diff-line-num new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Bio::WebAgent"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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41
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<td class="diff-line-num new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"CGI"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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42
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Cache::FileCache"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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43
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<td class="diff-line-num new_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Getopt::Long"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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44
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"HTTP::Request::Common"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"LWP::Protocol::https"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="45" 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">
45
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<td class="diff-line-num new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"LWP::UserAgent"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
</pre>
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46
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<td class="diff-line-num new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"URI"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="47" 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">
47
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"URI::Escape"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" 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="81" 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">@@ -79,7 +81,7 @@</td>
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79
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"web"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://github.com/bioperl/bio-db-ncbihelper"</span></span>
</pre>
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80
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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81
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">6</span>"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="83" 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">
83
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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"x_Dist_Zilla"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="84" 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">
84
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<td class="diff-line-num new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"perl"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<td class="diff-line-num new_line" data-linenumber="87" 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">
87
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC87" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"5.028001"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" 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="296" 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">@@ -294,7 +296,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="294" 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">
294
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<td class="diff-line-num new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"branch"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">null</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="295" 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">
295
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<td class="diff-line-num new_line" data-linenumber="297" 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">
297
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC297" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"changelog"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Changes"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="296" 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">
296
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<td class="diff-line-num new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"signed"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="297" 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">
297
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<td class="diff-line-num new_line old" data-linenumber="299" 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="LC297" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"tag"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Bio-DB-NCBIHelper-v1.7.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"tag"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Bio-DB-NCBIHelper-v1.7.<span class="idiff left right">6</span>"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="298" 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">
298
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<td class="diff-line-num new_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"tag_format"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"%N-v%v"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="299" 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">
299
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<td class="diff-line-num new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"tag_message"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"%N-v%v"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="300" 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">
300
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<td class="diff-line-num new_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" 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="311" 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">@@ -309,6 +311,17 @@</td>
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<td class="diff-line-num old_line" data-linenumber="309" 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">
309
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<td class="diff-line-num new_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"name"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"@BioPerl/Git::Tag"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="310" 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">
310
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<td class="diff-line-num new_line" data-linenumber="312" 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">
312
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC312" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2.045"</span></span>
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311
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<td class="diff-line-num new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC315" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"class"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Dist::Zilla::Plugin::Prereqs"</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"config"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="317" 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">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"Dist::Zilla::Plugin::Prereqs"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"phase"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"runtime"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"type"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"requires"</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="322" 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">
322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"name"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Prereqs"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="323" 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">
323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"6.012"</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="313" 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="LC326" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"class"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Dist::Zilla::Plugin::FinderCode"</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="314" 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="LC327" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"name"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">":InstallModules"</span><span class="p">,</span></span>
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<li id="3b7f8f92275828b66b32cb6c6aeb61e73c1d7587">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#3b7f8f92275828b66b32cb6c6aeb61e73c1d7587"><strong>META.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" 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">@@ -24,18 +24,20 @@ meta-spec:</td>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">1.4'</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bio-DB-NCBIHelper</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"><span class="na" style="color: #008080;">requires</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::DB::Query::WebQuery: <span class="idiff left right">'0'</span></span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::DB::Query::WebQuery: <span class="idiff left right">v1.7.7</span></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::DB::Taxonomy: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::DB::WebDBSeqI: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::Root::IO: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::Root::Root: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::SeqIO: '0'</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::SeqIO::entrezgene: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::Taxon: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"> <span class="s" style="color: #d14;">Bio::WebAgent: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="s" style="color: #d14;">CGI</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">0'</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"> <span class="s" style="color: #d14;">Cache::FileCache: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"> <span class="s" style="color: #d14;">Getopt::Long: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml"> <span class="s" style="color: #d14;">HTTP::Request::Common: '0'</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="s" style="color: #d14;">LWP::Protocol::https: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="s" style="color: #d14;">LWP::UserAgent: '0'</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">URI</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">0'</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="yaml"> <span class="s" style="color: #d14;">URI::Escape: '0'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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="51" 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">@@ -49,7 +51,7 @@ resources:</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">bugtracker</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://github.com/bioperl/bio-db-ncbihelper/issues</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">homepage</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://metacpan.org/release/Bio-DB-NCBIHelper</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">repository</span><span class="pi">:</span> <span class="s" style="color: #d14;">git://github.com/bioperl/bio-db-ncbihelper.git</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">6</span></span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="yaml"><span class="na" style="color: #008080;">x_Dist_Zilla</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">perl</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">5.028001'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" 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="220" 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">@@ -218,7 +220,7 @@ x_Dist_Zilla:</td>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="yaml"> <span class="s" style="color: #d14;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">~</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="yaml"> <span class="s" style="color: #d14;">changelog</span><span class="pi">:</span> <span class="s" style="color: #d14;">Changes</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="yaml"> <span class="s" style="color: #d14;">signed</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="yaml"> <span class="na" style="color: #008080;">tag</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bio-DB-NCBIHelper-v1.7.<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="yaml"> <span class="na" style="color: #008080;">tag</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bio-DB-NCBIHelper-v1.7.<span class="idiff left right">6</span></span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="yaml"> <span class="na" style="color: #008080;">tag_format</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">%N-v%v'</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="yaml"> <span class="na" style="color: #008080;">tag_message</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">%N-v%v'</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="yaml"> <span class="s" style="color: #d14;">Dist::Zilla::Role::Git::Repo:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" 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">@@ -228,6 +230,14 @@ x_Dist_Zilla:</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="yaml"> <span class="s" style="color: #d14;">time_zone</span><span class="pi">:</span> <span class="s" style="color: #d14;">local</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">@BioPerl/Git::Tag'</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">2.045'</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="yaml"> <span class="pi">-</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="yaml"> <span class="na" style="color: #008080;">class</span><span class="pi">:</span> <span class="s" style="color: #d14;">Dist::Zilla::Plugin::Prereqs</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="yaml"> <span class="na" style="color: #008080;">config</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="yaml"> <span class="s" style="color: #d14;">Dist::Zilla::Plugin::Prereqs:</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="yaml"> <span class="s" style="color: #d14;">phase</span><span class="pi">:</span> <span class="s" style="color: #d14;">runtime</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="yaml"> <span class="s" style="color: #d14;">type</span><span class="pi">:</span> <span class="s" style="color: #d14;">requires</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Prereqs</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">6.012'</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="yaml"> <span class="pi">-</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="yaml"> <span class="na" style="color: #008080;">class</span><span class="pi">:</span> <span class="s" style="color: #d14;">Dist::Zilla::Plugin::FinderCode</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">:InstallModules'</span></span>
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<li id="a6a4139b0f32af1594c237ebe008acaf8217f505">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#a6a4139b0f32af1594c237ebe008acaf8217f505"><strong>Makefile.PL</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,18 +22,20 @@ my %WriteMakefileArgs = (</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"> <span class="s2" style="color: #d14;">"MIN_PERL_VERSION"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"5.006"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"> <span class="s2" style="color: #d14;">"NAME"</span> <span class="nl">=> "Bio</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">DB::NCBIHelper"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"> <span class="s2" style="color: #d14;">"PREREQ_PM"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::Query::WebQuery"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">0</span>,</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::Query::WebQuery"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;"><span class="idiff left right">"1.7.7"</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></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">
26
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<td class="diff-line-num new_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">
26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::Taxonomy"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num old_line" data-linenumber="27" 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">
27
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<td class="diff-line-num new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::WebDBSeqI"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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28
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<td class="diff-line-num new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::Root::IO"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
29
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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::Root::Root"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num old_line" data-linenumber="30" 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">
30
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<td class="diff-line-num new_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::SeqIO"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::SeqIO::entrezgene"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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31
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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::Taxon"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
32
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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::WebAgent"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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33
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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
34
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"> <span class="s2" style="color: #d14;">"CGI"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
34
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<td class="diff-line-num new_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"> <span class="s2" style="color: #d14;">"Cache::FileCache"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
</pre>
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35
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<td class="diff-line-num new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"> <span class="s2" style="color: #d14;">"Getopt::Long"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="36" 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">
36
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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"> <span class="s2" style="color: #d14;">"HTTP::Request::Common"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"> <span class="s2" style="color: #d14;">"LWP::Protocol::https"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
37
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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"> <span class="s2" style="color: #d14;">"LWP::UserAgent"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="38" 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">
38
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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"> <span class="s2" style="color: #d14;">"URI"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
</pre>
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39
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<td class="diff-line-num new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"> <span class="s2" style="color: #d14;">"URI::Escape"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,7 +55,7 @@ my %WriteMakefileArgs = (</td>
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53
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55
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC55" class="line" lang="make"> <span class="s2" style="color: #d14;">"Test::Most"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="54" 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">
54
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<td class="diff-line-num new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="make"> <span class="s2" style="color: #d14;">"Test::RequiresInternet"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span></span>
</pre>
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55
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">},</span></span>
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56
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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC56" class="line" lang="make"> <span class="s2" style="color: #d14;">"VERSION"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">4</span>"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="make"> <span class="s2" style="color: #d14;">"VERSION"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">6</span>"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>
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57
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="make"> <span class="s2" style="color: #d14;">"test"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"> <span class="s2" style="color: #d14;">"TESTS"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"t/*.t"</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">}</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">@@ -61,12 +63,13 @@ my %WriteMakefileArgs = (</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="make"></span>
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62
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"></span>
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63
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span><span class="nv" style="color: #008080;">FallbackPrereqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::Query::WebQuery"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">0</span>,</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::Query::WebQuery"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;"><span class="idiff left right">"1.7.7"</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>
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65
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::Taxonomy"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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66
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::DB::WebDBSeqI"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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67
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::Root::IO"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::Root::Root"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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69
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::SeqIO"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::SeqIO::entrezgene"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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70
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::Taxon"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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71
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="make"> <span class="s2" style="color: #d14;">"Bio::WebAgent"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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72
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="make"> <span class="s2" style="color: #d14;">"CGI"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" 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">@@ -76,6 +79,7 @@ my %FallbackPrereqs = (</td>
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76
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="make"> <span class="s2" style="color: #d14;">"HTTP::Request::Common"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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77
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="make"> <span class="s2" style="color: #d14;">"IO::Handle"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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78
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="make"> <span class="s2" style="color: #d14;">"IPC::Open3"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="make"> <span class="s2" style="color: #d14;">"LWP::Protocol::https"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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79
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<td class="diff-line-num new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="make"> <span class="s2" style="color: #d14;">"LWP::UserAgent"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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80
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="make"> <span class="s2" style="color: #d14;">"Test::Exception"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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81
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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="make"> <span class="s2" style="color: #d14;">"Test::More"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>
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<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#384adeead2ae33537082bc3db4b10a27220e76ca"><strong>dist.ini</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="ini"><span class="py">name</span> <span class="p">=</span> <span class="s" style="color: #d14;">Bio-DB-NCBIHelper</span></span>
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2
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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="ini"><span class="py">version</span> <span class="p">=</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">4</span></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="ini"><span class="py">version</span> <span class="p">=</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">6</span></span></span>
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3
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<td class="diff-line-num new_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="ini"><span class="py">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">Aaron Mackey <amackey@virginia.edu></span></span>
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4
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="ini"><span class="py">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">Brian Osborne <bosborne@alum.mit.edu></span></span>
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<td class="diff-line-num old_line" data-linenumber="5" 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">
5
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<td class="diff-line-num new_line" data-linenumber="5" 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">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="ini"><span class="py">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">Jason Stajich <jason@bioperl.org></span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,3 +13,8 @@ license = Perl_5</td>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="ini"><span class="py">-remove</span> <span class="p">=</span> <span class="s" style="color: #d14;">PodWeaver</span></span>
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14
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<td class="diff-line-num 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="ini"><span class="py">-remove</span> <span class="p">=</span> <span class="s" style="color: #d14;">Test::EOL</span></span>
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15
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<td class="diff-line-num new_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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="ini"><span class="py">-remove</span> <span class="p">=</span> <span class="s" style="color: #d14;">Test::NoTabs</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="ini"></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="ini"><span class="nn" style="color: #555;">[Prereqs]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="ini"><span class="err" style="color: #a61717; background-color: #e3d2d2;">Bio::DB::Query::</span><span class="py">WebQuery</span> <span class="p">=</span> <span class="s" style="color: #d14;">1.7.7</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="ini"><span class="err" style="color: #a61717; background-color: #e3d2d2;">Bio::SeqIO::</span><span class="py">entrezgene</span> <span class="p">=</span> <span class="s" style="color: #d14;">0</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="ini"><span class="err" style="color: #a61717; background-color: #e3d2d2;">LWP::Protocol::</span><span class="py">https</span> <span class="p">=</span> <span class="s" style="color: #d14;">0</span></span></pre>
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<li id="88a8729aee4b852e491f1f6e67064c25fdc872ec">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#88a8729aee4b852e491f1f6e67064c25fdc872ec"><strong>lib/Bio/DB/EntrezGene.pm</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">@@ -93,7 +93,7 @@ methods. Internal methods are usually preceded with a _</td>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">EntrezGene</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::EntrezGene::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::EntrezGene::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">6</span></span><span class="p">';</span></span>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw($DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#a84412d8551a98a5524a93620ede1b428d2395bd"><strong>lib/Bio/DB/GenBank.pm</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -165,7 +165,7 @@ preceded with a _</td>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::GenBank::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::GenBank::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">6</span></span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw(%PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#aff401a99f6558c2d03e3f3b80e58ab886212a13"><strong>lib/Bio/DB/GenPept.pm</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,7 +93,7 @@ methods. Internal methods are usually preceded with a _</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenPept</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::GenPept::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::GenPept::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">6</span></span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw($DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#002bf5ec2dc04ef6165f2361f313f45e3b0ac7ca"><strong>lib/Bio/DB/NCBIHelper.pm</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,7 +85,7 @@ preceded with a _</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">NCBIHelper</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::NCBIHelper::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::NCBIHelper::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">6</span></span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::DB::Query::</span><span class="nv" style="color: #008080;">GenBank</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -261,6 +261,7 @@ sub get_request {</td>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$format</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-email</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$email</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="perl"> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_sleep</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_request</span><span class="p">(</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">qualifiers</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</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">@@ -269,6 +270,116 @@ sub get_request {</td>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="perl"></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 get_seq_stream</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="perl"></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Title : get_seq_stream</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Usage : my $seqio = $self->get_seq_stream(%qualifiers)</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Function: builds a url and queries a web db</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Returns : a Bio::SeqIO stream capable of producing sequence</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Args : %qualifiers = a hash qualifiers that the implementing class</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> will process to make a url suitable for web querying</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="perl"></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=cut</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="perl"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">get_seq_stream</span> <span class="p">{</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">qualifiers</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@_</span><span class="p">;</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$rformat</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ioformat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">request_format</span><span class="p">();</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">qualifiers</span> <span class="p">)</span> <span class="p">{</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$key</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/format/i</span> <span class="p">)</span> <span class="p">{</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="perl"> <span class="nv" style="color: #008080;">$rformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$qualifiers</span><span class="p">{</span><span class="nv" style="color: #008080;">$key</span><span class="p">};</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="perl"> <span class="nv" style="color: #008080;">$seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="perl"> <span class="p">}</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="perl"> <span class="p">}</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="perl"> <span class="nv" style="color: #008080;">$qualifiers</span><span class="p">{'</span><span class="s1" style="color: #d14;">-format</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$rformat</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$seen</span><span class="p">);</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$rformat</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ioformat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">request_format</span><span class="p">(</span><span class="nv" style="color: #008080;">$rformat</span><span class="p">);</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># These parameters are implemented for Bio::DB::GenBank objects only</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">isa</span><span class="p">('</span><span class="s1" style="color: #d14;">Bio::DB::GenBank</span><span class="p">'))</span> <span class="p">{</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq_start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$qualifiers</span><span class="p">{'</span><span class="s1" style="color: #d14;">-seq_start</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq_start</span><span class="p">());</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq_stop</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$qualifiers</span><span class="p">{'</span><span class="s1" style="color: #d14;">-seq_stop</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq_stop</span><span class="p">());</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">strand</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$qualifiers</span><span class="p">{'</span><span class="s1" style="color: #d14;">-strand</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">strand</span><span class="p">());</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">email</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$qualifiers</span><span class="p">{'</span><span class="s1" style="color: #d14;">-email</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">email</span><span class="p">());</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">complexity</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$qualifiers</span><span class="p">{'</span><span class="s1" style="color: #d14;">-complexity</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">complexity</span><span class="p">());</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="perl"> <span class="p">}</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$request</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_request</span><span class="p">(</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">qualifiers</span><span class="p">);</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="perl"> <span class="nv" style="color: #008080;">$request</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">proxy_authorization_basic</span><span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">authentication</span><span class="p">)</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">authentication</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" 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">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">debug</span><span class="p">("</span><span class="s2" style="color: #d14;">request is </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$request</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">as_string</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="perl"></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># workaround for MSWin systems</span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">retrieval_type</span><span class="p">('</span><span class="s1" style="color: #d14;">io_string</span><span class="p">')</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">retrieval_type</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/pipeline/</span> <span class="o" style="font-weight: 600;">&&</span> <span class="vg" style="color: #008080;">$^O</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^MSWin/</span><span class="p">;</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">retrieval_type</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/pipeline/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Try to create a stream using POSIX fork-and-pipe facility.</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># this is a *big* win when fetching thousands of sequences from</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># a web database because we can return the first entry while</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># transmission is still in progress.</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Also, no need to keep sequence in memory or in a temporary file.</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># If this fails (Windows, MacOS 9), we fall back to non-pipelined access.</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># fork and pipe: _stream_request()=><STREAM></span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$result</span><span class="p">,</span><span class="nv" style="color: #008080;">$stream</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_open_pipe</span><span class="p">();</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="perl"></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$result</span><span class="p">)</span> <span class="p">{</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">DB::</span><span class="nv" style="color: #008080;">fork_TTY</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Spec</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">devnull</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># prevents complaints from debugger</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$result</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># in child process</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_stream_request</span><span class="p">(</span><span class="nv" style="color: #008080;">$request</span><span class="p">,</span><span class="nv" style="color: #008080;">$stream</span><span class="p">);</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="perl"> <span class="nn" style="color: #555;">POSIX::</span><span class="nv" style="color: #008080;">_exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">#prevent END blocks from executing in this forked child</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="perl"> <span class="p">}</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-verbose</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">verbose</span><span class="p">,</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$ioformat</span><span class="p">,</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-fh</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$stream</span><span class="p">);</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="perl"> <span class="p">}</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="perl"> <span class="p">}</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">retrieval_type</span><span class="p">('</span><span class="s1" style="color: #d14;">io_string</span><span class="p">');</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="perl"> <span class="p">}</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="perl"> <span class="p">}</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="perl"></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">retrieval_type</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/temp/i</span><span class="p">)</span> <span class="p">{</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">io</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tempdir</span><span class="p">(</span> <span class="nv" style="color: #008080;">CLEANUP</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$fh</span><span class="p">,</span> <span class="nv" style="color: #008080;">$tmpfile</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">io</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tempfile</span><span class="p">(</span> <span class="nv" style="color: #008080;">DIR</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$dir</span> <span class="p">);</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: #008080;">$fh</span><span class="p">;</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$resp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_request</span><span class="p">(</span><span class="nv" style="color: #008080;">$request</span><span class="p">,</span> <span class="nv" style="color: #008080;">$tmpfile</span><span class="p">);</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$tmpfile</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">z</span> <span class="nv" style="color: #008080;">$tmpfile</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: #008080;">$resp</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_success</span><span class="p">()</span> <span class="p">)</span> <span class="p">{</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">throw</span><span class="p">("</span><span class="s2" style="color: #d14;">WebDBSeqI Error - check query sequences!</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="perl"> <span class="p">}</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">postprocess_data</span><span class="p">('</span><span class="s1" style="color: #d14;">type</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">file</span><span class="p">',</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">location</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$tmpfile</span><span class="p">);</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># this may get reset when requesting batch mode</span></span>
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<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$rformat</span><span class="p">,</span><span class="nv" style="color: #008080;">$ioformat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">request_format</span><span class="p">();</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ERR</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;"><</span><span class="p">',</span> <span class="nv" style="color: #008080;">$tmpfile</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">throw</span><span class="p">("</span><span class="s2" style="color: #d14;">Could not read file '</span><span class="si" style="color: #d14;">$tmpfile</span><span class="s2" style="color: #d14;">': $!</span><span class="p">");</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$ERR</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">debug</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">);}</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: #008080;">$ERR</span><span class="p">;</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="perl"> <span class="p">}</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="perl"></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-verbose</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">verbose</span><span class="p">,</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$ioformat</span><span class="p">,</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-file</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$tmpfile</span><span class="p">);</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="perl"> <span class="p">}</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="perl"></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">retrieval_type</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/io_string/i</span> <span class="p">)</span> <span class="p">{</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$resp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_request</span><span class="p">(</span><span class="nv" style="color: #008080;">$request</span><span class="p">);</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$content</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$resp</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">content_ref</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">debug</span><span class="p">(</span> <span class="p">"</span><span class="s2" style="color: #d14;">content is $</span><span class="si" style="color: #d14;">$content</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$resp</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_success</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$$content</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">throw</span><span class="p">("</span><span class="s2" style="color: #d14;">WebDBSeqI Error - check query sequences!</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="perl"> <span class="p">}</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$rformat</span><span class="p">,</span><span class="nv" style="color: #008080;">$ioformat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">request_format</span><span class="p">();</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">postprocess_data</span><span class="p">('</span><span class="s1" style="color: #d14;">type</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">string</span><span class="p">',</span></span>
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<td class="diff-line-num new new_line" data-linenumber="372" 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">
372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">location</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$content</span><span class="p">);</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">debug</span><span class="p">(</span> <span class="p">"</span><span class="s2" style="color: #d14;">str is $</span><span class="si" style="color: #d14;">$content</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="374" 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">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-verbose</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">verbose</span><span class="p">,</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$ioformat</span><span class="p">,</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-fh</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="k" style="font-weight: 600;">new</span> <span class="nn" style="color: #555;">IO::</span><span class="nv" style="color: #008080;">String</span><span class="p">(</span><span class="nv" style="color: #008080;">$$content</span><span class="p">));</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="perl"> <span class="p">}</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="perl"></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if we got here, we don't know how to handle the retrieval type</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">throw</span><span class="p">("</span><span class="s2" style="color: #d14;">retrieval type </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">retrieval_type</span> <span class="o" style="font-weight: 600;">.</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="perl"> <span class="p">"</span><span class="s2" style="color: #d14;"> unsupported</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="perl"><span class="p">}</span></span>
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272
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="perl"></span>
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273
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 get_Stream_by_batch</span></span>
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274
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="perl"></span>
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<li id="08f0cedb845978af21d4ee7737d5850f52129211">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#08f0cedb845978af21d4ee7737d5850f52129211"><strong>lib/Bio/DB/Query/GenBank.pm</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># BioPerl module for Bio::DB::Query::GenBank.pm</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Please direct questions and support issues to <bioperl-l@bioperl.org><span class="idiff left right"> </span></span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Please direct questions and support issues to <bioperl-l@bioperl.org></span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Cared for by Lincoln Stein <lstein@cshl.org></span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</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">@@ -62,15 +62,15 @@ is much appreciated.</td>
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62
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> bioperl-l@bioperl.org - General discussion</span></span>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> http://bioperl.org/wiki/Mailing_lists - About the mailing lists</span></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="perl"></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 Support<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 Support</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Please direct usage questions or support issues to the mailing list:</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">I<bioperl-l@bioperl.org></span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">rather than to the module maintainer directly. Many experienced and<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">reponsive experts will be able look at the problem and quickly<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">address it. Please include a thorough description of the problem<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">rather than to the module maintainer directly. Many experienced and</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">reponsive experts will be able look at the problem and quickly</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">address it. Please include a thorough description of the problem</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">with code and data examples if at all possible.</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 Reporting Bugs</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">@@ -96,7 +96,7 @@ preceded with a _</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::DB::Query::</span><span class="nv" style="color: #008080;">GenBank</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::Query::GenBank::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::Query::GenBank::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">6</span></span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">URI::</span><span class="nv" style="color: #008080;">Escape</span> <span class="p">'</span><span class="s1" style="color: #d14;">uri_unescape</span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">NCBIHelper</span><span class="p">;</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">@@ -104,7 +104,7 @@ use Bio::DB::NCBIHelper;</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#use constant EPOST => $Bio::DB::NCBIHelper::HOSTBASE . '/entrez/eutils/epost.fcgi';</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#use constant ESEARCH => $Bio::DB::NCBIHelper::HOSTBASE . '/entrez/eutils/esearch.fcgi';</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># the reference to the our variable of the $Bio::DB::NCBIHelper::HOSTBASE doesn't seem to work in<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># the reference to the our variable of the $Bio::DB::NCBIHelper::HOSTBASE doesn't seem to work in</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># the constant definition in perl 5.10.1 or 5.16.3</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">constant</span> <span class="nv" style="color: #008080;">EPOST</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">/entrez/eutils/epost.fcgi</span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">constant</span> <span class="nv" style="color: #008080;">ESEARCH</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">/entrez/eutils/esearch.fcgi</span><span class="p">';</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">@@ -112,11 +112,12 @@ use constant DEFAULT_DB => 'protein';</td>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">constant</span> <span class="nv" style="color: #008080;">MAXENTRY</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw(@ATTRIBUTES)</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$REQUEST_DELAY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">base</span> <span class="sx" style="color: #d14;">qw(Bio::DB::Query::WebQuery)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="perl"><span class="k" style="font-weight: 600;">BEGIN</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="perl"> <span class="nv" style="color: #008080;">@ATTRIBUTES</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qw(db reldate mindate maxdate datetype maxids)</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"> <span class="nv" style="color: #008080;">@ATTRIBUTES</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qw(db reldate mindate maxdate datetype maxids<span class="idiff left right"> email</span>)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$method</span> <span class="p">(</span><span class="nv" style="color: #008080;">@ATTRIBUTES</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s" style="color: #d14;"><<END;</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="perl"><span class="s" style="color: #d14;">sub $method {</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">@@ -144,6 +145,10 @@ END</td>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> -ids array ref of gids (overrides query)</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> -maxids the maximum number of IDs you wish to collect</span></span>
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146
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> (defaults to 100)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> -email Email address; required if you want to decrease</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> delay time between queries</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> -delay Delay time (in seconds). Note NCBI policy requires 4</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> seconds between requests unless an email is provided</span></span>
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147
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">This method creates a new query object. Typically you will specify a</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">-db and a -query argument, possibly modified by -mindate, -maxdate, or</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" 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="194" 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">@@ -189,13 +194,15 @@ receive when you generate a SeqIO stream from the query.</td>
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189
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">new</span> <span class="p">{</span></span>
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190
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$class</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$self</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$class</span><span class="o" style="font-weight: 600;">-></span><span class="nn" style="color: #555;">SUPER::</span><span class="nv" style="color: #008080;">new</span><span class="p">(</span><span class="nv" style="color: #008080;">@_</span><span class="p">);</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">,</span><span class="nv" style="color: #008080;">$db</span><span class="p">,</span><span class="nv" style="color: #008080;">$reldate</span><span class="p">,</span><span class="nv" style="color: #008080;">$mindate</span><span class="p">,</span><span class="nv" style="color: #008080;">$maxdate</span><span class="p">,</span><span class="nv" style="color: #008080;">$datetype</span><span class="p">,</span><span class="nv" style="color: #008080;">$ids</span><span class="p">,</span><span class="nv" style="color: #008080;">$maxids</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="perl"> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_rearrange</span><span class="p">([</span><span class="sx" style="color: #d14;">qw(QUERY DB RELDATE MINDATE MAXDATE DATETYPE IDS MAXIDS)</span><span class="p">],</span><span class="nv" style="color: #008080;">@_</span><span class="p">);</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">,</span><span class="nv" style="color: #008080;">$db</span><span class="p">,</span><span class="nv" style="color: #008080;">$reldate</span><span class="p">,</span><span class="nv" style="color: #008080;">$mindate</span><span class="p">,</span><span class="nv" style="color: #008080;">$maxdate</span><span class="p">,</span><span class="nv" style="color: #008080;">$datetype</span><span class="p">,</span><span class="nv" style="color: #008080;">$ids</span><span class="p">,</span><span class="nv" style="color: #008080;">$maxids</span><span class="p">,</span><span class="nv" style="color: #008080;">$email</span><span class="p">,</span><span class="nv" style="color: #008080;">$delay</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="perl"> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_rearrange</span><span class="p">([</span><span class="sx" style="color: #d14;">qw(QUERY DB RELDATE MINDATE MAXDATE DATETYPE IDS</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="perl"><span class="sx" style="color: #d14;"> MAXIDS EMAIL DELAY)</span><span class="p">],</span><span class="nv" style="color: #008080;">@_</span><span class="p">);</span></span>
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194
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">db</span><span class="p">(</span><span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">DEFAULT_DB</span><span class="p">);</span></span>
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195
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="perl"> <span class="nv" style="color: #008080;">$reldate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">reldate</span><span class="p">(</span><span class="nv" style="color: #008080;">$reldate</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
196
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<td class="diff-line-num new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="perl"> <span class="nv" style="color: #008080;">$mindate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">mindate</span><span class="p">(</span><span class="nv" style="color: #008080;">$mindate</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="197" 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">
197
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<td class="diff-line-num new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="perl"> <span class="nv" style="color: #008080;">$maxdate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">maxdate</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxdate</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
198
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="perl"> <span class="nv" style="color: #008080;">$maxids</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">maxids</span><span class="p">(</span><span class="nv" style="color: #008080;">$maxids</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="perl"> <span class="nv" style="color: #008080;">$email</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">email</span><span class="p">(</span><span class="nv" style="color: #008080;">$email</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
199
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="perl"> <span class="nv" style="color: #008080;">$datetype</span> <span class="o" style="font-weight: 600;">||=</span> <span class="p">'</span><span class="s1" style="color: #d14;">mdat</span><span class="p">';</span></span>
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200
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="perl"> <span class="nv" style="color: #008080;">$datetype</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">datetype</span><span class="p">(</span><span class="nv" style="color: #008080;">$datetype</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="222" 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="229" 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">@@ -222,6 +229,7 @@ sub cookie {</td>
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222
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="223" 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">
223
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="224" 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">
224
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_sleep</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
225
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_run_query</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="226" 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">
226
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<td class="diff-line-num new_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="perl"> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="p">}{</span><span class="sx" style="color: #d14;">qw(_cookie _querynum)</span><span class="p">};</span></span>
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<td class="diff-line-num old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
227
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="243" 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="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -243,11 +251,14 @@ sub _request_parameters {</td>
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243
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<td class="diff-line-num new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@params</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">eval</span><span class="p">("</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$self</span><span class="s2" style="color: #d14;">-></span><span class="si" style="color: #d14;">$_</span><span class="p">")</span> <span class="p">?</span> <span class="p">(</span><span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=></span> <span class="nb" style="color: #0086b3;">eval</span><span class="p">("</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$self</span><span class="s2" style="color: #d14;">-></span><span class="si" style="color: #d14;">$_</span><span class="p">"))</span> <span class="p">:</span> <span class="p">()</span> <span class="p">}</span> <span class="nv" style="color: #008080;">@ATTRIBUTES</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="244" 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">
244
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<td class="diff-line-num new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: #008080;">@params</span><span class="p">,('</span><span class="s1" style="color: #d14;">usehistory</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">y</span><span class="p">','</span><span class="s1" style="color: #d14;">tool</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">bioperl</span><span class="p">');</span></span>
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245
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="perl"> <span class="nv" style="color: #008080;">$method</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">get</span><span class="p">';</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="perl"><span class="idiff left right"> </span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="perl"></span>
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247
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="perl"> <span class="nv" style="color: #008080;">$base</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::NCBIHelper::</span><span class="nv" style="color: #008080;">HOSTBASE</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">ESEARCH</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># this seems to need to be dynamic</span></span>
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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
248
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: #008080;">@params</span><span class="p">,('</span><span class="s1" style="color: #d14;">term</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">query</span><span class="p">);</span></span>
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249
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<td class="diff-line-num new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Providing 'retmax' limits queries to 500 sequences ?? I don't think so LS</span></span>
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<td class="diff-line-num old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
250
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<td class="diff-line-num new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: #008080;">@params</span><span class="p">,('</span><span class="s1" style="color: #d14;">retmax</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">maxids</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">MAXENTRY</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">email</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: #008080;">@params</span><span class="p">,('</span><span class="s1" style="color: #d14;">email</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">email</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="perl"> <span class="p">}</span></span>
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251
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="252" 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">
252
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<td class="diff-line-num new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># And actually, it seems that we need 'retstart' equal to 0 ?? I don't think so LS</span></span>
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253
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># push @params, ('retstart' => 0);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="276" 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="287" 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">@@ -276,6 +287,7 @@ sub count {</td>
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276
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$d</span><span class="p">;</span></span>
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277
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="278" 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">
278
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<td class="diff-line-num new_line" data-linenumber="289" 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="LC289" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_sleep</span><span class="p">();</span></span>
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279
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_run_query</span><span class="p">;</span></span>
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280
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{'</span><span class="s1" style="color: #d14;">_count</span><span class="p">'};</span></span>
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281
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -357,4 +369,22 @@ sub _generate_id_string {</td>
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357
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="perl"> <span class="p">}</span> <span class="nv" style="color: #008080;">@$ids</span><span class="p">));</span></span>
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358
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="perl"><span class="p">}</span></span>
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359
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="perl"></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 delay_policy</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Title : delay_policy</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Usage : $secs = $self->delay_policy</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Function: NCBI requests a delay of 4 seconds between requests unless email is</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> provided. This method implements a 4 second delay; use 'delay()' to</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> override, though understand if no email is provided we are not</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> responsible for users being IP-blocked by NCBI</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Returns : number of seconds to delay</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"> Args : none</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="perl"></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=cut</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="perl"></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">delay_policy</span> <span class="p">{</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$self</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$REQUEST_DELAY</span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="perl"><span class="p">}</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="perl"></span>
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360
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="perl"><span class="mi" style="color: #099;">1</span><span class="p">;</span></span></pre>
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<li id="f85d1f5169454d0f079cda8a369165345bd7c6d9">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#f85d1f5169454d0f079cda8a369165345bd7c6d9"><strong>lib/Bio/DB/Taxonomy/entrez.pm</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">@@ -101,7 +101,7 @@ Internal methods are usually preceded with a _</td>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="perl"></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::DB::Taxonomy::</span><span class="nv" style="color: #008080;">entrez</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::Taxonomy::entrez::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::DB::Taxonomy::entrez::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">6</span></span><span class="p">';</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw($EntrezLocation $UrlParamSeparatorValue %EntrezParams</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl"><span class="sx" style="color: #d14;"> $EntrezGet $EntrezSummary $EntrezFetch %SequenceParams</span></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="perl"><span class="sx" style="color: #d14;"> $XMLTWIG $DATA_CACHE $RELATIONS)</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,7 +168,7 @@ sub _initialize {</td>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nn" style="color: #555;">SUPER::</span><span class="nv" style="color: #008080;">_initialize</span><span class="p">(</span><span class="nv" style="color: #008080;">@_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="perl"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$location</span><span class="p">,</span><span class="nv" style="color: #008080;">$params</span><span class="p"><span class="idiff left">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">_rearrange</span></span><span class="p"><span class="idiff">([</span></span><span class="sx" style="color: #d14;"><span class="idiff right">qw(LOCATION PARAMS</span>)</span><span class="p">],</span><span class="nv" style="color: #008080;">@_</span><span class="p">);</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$location</span><span class="p">,</span><span class="nv" style="color: #008080;">$params</span><span class="p"><span class="idiff left">,</span></span><span class="nv" style="color: #008080;"><span class="idiff">$email</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">_rearrange</span></span><span class="p"><span class="idiff">([</span></span><span class="sx" style="color: #d14;"><span class="idiff right">qw(LOCATION PARAMS EMAIL</span>)</span><span class="p">],</span><span class="nv" style="color: #008080;">@_</span><span class="p">);</span></span>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="perl"></span>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$params</span> <span class="p">)</span> <span class="p">{</span></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">ref</span><span class="p">(</span><span class="nv" style="color: #008080;">$params</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">/HASH/i</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,6 +178,9 @@ sub _initialize {</td>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">\%</span><span class="nv" style="color: #008080;">EntrezParams</span><span class="p">;</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$email</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">email</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$email</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="perl"> <span class="p">}</span></span>
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181
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">entrez_params</span><span class="p">(</span><span class="nv" style="color: #008080;">$params</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">entrez_url</span><span class="p">(</span><span class="nv" style="color: #008080;">$location</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$EntrezLocation</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="perl"><span class="p">}</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">@@ -593,7 +596,6 @@ sub entrez_params{</td>
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">$f</span><span class="p">;</span></span>
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="perl"><span class="p">}</span></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="perl"></span>
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 Bio::DB::WebBase methods</span></span>
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="perl"></span>
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 proxy_string</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">@@ -667,6 +669,7 @@ sub _run_query {</td>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Given an eutil url, run the eutil query and parse the response into an</span></span>
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668
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670
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># XML Twig object</span></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="p">,</span> <span class="nv" style="color: #008080;">$url</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">sleep</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$response</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get</span><span class="p">(</span><span class="nv" style="color: #008080;">$url</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$response</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">is_success</span><span class="p">)</span> <span class="p">{</span></span>
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675
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="perl"> <span class="nv" style="color: #008080;">$response</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$response</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">content</span><span class="p">;</span></span>
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<li id="75a796bca1acd6cefec2fb423331df522d057729">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#75a796bca1acd6cefec2fb423331df522d057729"><strong>t/EntrezGene.t</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,8 +10,18 @@ BEGIN {</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"> <span class="nv" style="color: #008080;">use_ok</span><span class="p">('</span><span class="s1" style="color: #d14;">Bio::DB::EntrezGene</span><span class="p">');</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">})</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-email</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-delay</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"><span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-verbose</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLDEBUG</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$gb</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seqio</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">EntrezGene</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">retrievaltype</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">tempfile</span><span class="p">',</span> <span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">delay</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">EntrezGene</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">retrievaltype</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">tempfile</span><span class="p">',</span> <span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Bio::DB::EntrezGene</span></span>
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<li id="96ec5a5ce3dd8358677c3c1f0d8596336500eb52">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#96ec5a5ce3dd8358677c3c1f0d8596336500eb52"><strong>t/GenBank.t</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">@@ -21,11 +21,20 @@ my %expected_lengths = (</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$gb</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seqio</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seqin</span><span class="p">);</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">})</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-email</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-delay</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-verbose</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLDEBUG</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Bio::DB::GenBank</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(),</span> <span class="p">'</span><span class="s1" style="color: #d14;">Bio::DB::GenBank</span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">),</span> <span class="p">'</span><span class="s1" style="color: #d14;">Bio::DB::GenBank</span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># get a single seq</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</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">@@ -48,7 +57,7 @@ $seq = $seqio = undef;</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># batch mode</span></span>
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49
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Stream_by_id</span><span class="p">([</span><span class="sx" style="color: #d14;">qw(J00522 AF303112 2981014)</span><span class="p">]);};</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Batch access test failed for Genbank. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Batch access test failed for Genbank. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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52
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$done</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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53
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">next_seq</span><span class="p">)</span> <span class="p">{</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,23 +70,24 @@ SKIP: {</td>
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61
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="perl"><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span></span>
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62
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="perl"></span>
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63
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># test the temporary file creation and fasta</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">fasta</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">-retrievaltype</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">tempfile</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">-delay</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">fasta</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">-retrievaltype</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">tempfile</span><span class="p">',</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">),</span> </span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="perl"> <span class="p">"</span><span class="s2" style="color: #d14;">Tempfile tests</span><span class="p">";</span></span>
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65
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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66
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_id</span><span class="p">('</span><span class="s1" style="color: #d14;">J00522</span><span class="p">');};</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">6</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">6</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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68
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># last part of id holds the key</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\|/</span><span class="p">,</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">))[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]},</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\|/</span><span class="p">,</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">))[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]},</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check tmpfile: get_Seq_by_id:</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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70
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_acc</span><span class="p">('</span><span class="s1" style="color: #d14;">AF303112</span><span class="p">');};</span></span>
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71
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<td class="diff-line-num new_line old" data-linenumber="81" 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="LC71" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">5</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">5</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># last part of id holds the key</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\|/</span><span class="p">,</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">))[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]},</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\|/</span><span class="p">,</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">))[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]},</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check tmpfile: get_Seq_by_acc:</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># batch mode requires genbank format</span></span>
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75
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="perl"> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">request_format</span><span class="p">("</span><span class="s2" style="color: #d14;">gb</span><span class="p">");</span></span>
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76
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Stream_by_id</span><span class="p">([</span><span class="sx" style="color: #d14;">qw(J00522 AF303112 2981014)</span><span class="p">]);};</span></span>
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77
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<td class="diff-line-num new_line old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank batch tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank batch tests with a tempfile with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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78
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$done</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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79
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">next_seq</span><span class="p">)</span> <span class="p">{</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">}<span class="idiff left">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check tmpfile: get_Stream_by_id:</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$s</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff right">display_id</span></span><span class="p">;</span></span>
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81
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">undef</span> <span class="nv" style="color: #008080;">$gb</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># test the case where the db is gone,</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># but a temp file should remain until seqio goes away.</span></span>
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83
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="perl"> <span class="nv" style="color: #008080;">$done</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" 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="99" 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">@@ -89,19 +99,19 @@ SKIP: {</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="perl"><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span></span>
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90
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="perl"></span>
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91
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># test pipeline creation</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-retrievaltype</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">pipeline</span><span class="p">',</span> <span class="p"><span class="idiff left">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">-delay</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-retrievaltype</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">pipeline</span><span class="p">',</span> <span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff">params</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Pipeline tests</span></span><span class="p"><span class="idiff right">"</span>;</span></span>
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93
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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94
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<td class="diff-line-num new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_id</span><span class="p">('</span><span class="s1" style="color: #d14;">J00522</span><span class="p">');};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="95" 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">
95
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<td class="diff-line-num new_line old" data-linenumber="105" 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="LC95" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">6</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">6</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check pipeline: get_Seq_by_id:</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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97
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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_acc</span><span class="p">('</span><span class="s1" style="color: #d14;">AF303112</span><span class="p">');};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="98" 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">
98
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<td class="diff-line-num new_line old" data-linenumber="108" 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="LC98" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">5</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
99
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<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">5</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check pipeline: get_Seq_by_acc:</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="100" 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">
100
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<td class="diff-line-num new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Stream_by_id</span><span class="p">([</span><span class="sx" style="color: #d14;">qw(J00522 AF303112 2981014)</span><span class="p">]);};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="101" 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">
101
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<td class="diff-line-num new_line old" data-linenumber="111" 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="LC101" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests with a pipeline with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
</pre>
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102
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$done</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">next_seq</span><span class="p">)</span> <span class="p">{</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check pipeline: get_Stream_by_id:</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$s</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">undef</span> <span class="nv" style="color: #008080;">$gb</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># test the case where the db is gone,</span></span>
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106
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># but the pipeline should remain until seqio goes away</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"> <span class="nv" style="color: #008080;">$done</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,32 +123,32 @@ SKIP: {</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="perl"><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># test contig retrieval</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-<span class="idiff left">delay</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">-format</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">gbwithparts</span></span><span class="p"><span class="idiff right">'</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-<span class="idiff left">format</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">gbwithparts</span></span><span class="p"><span class="idiff">',</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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117
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_id</span><span class="p">('</span><span class="s1" style="color: #d14;">JH374761</span><span class="p">');};</span></span>
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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check contig: get_Seq_by_id:</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># now to check that postprocess_data in NCBIHelper catches CONTIG...</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-<span class="idiff left">delay</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">-format</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">gb</span></span><span class="p"><span class="idiff right">'</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-<span class="idiff left">format</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">gb</span></span><span class="p"><span class="idiff">',</span></span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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123
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_id</span><span class="p">('</span><span class="s1" style="color: #d14;">JH374761</span><span class="p">');};</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to GenBank with Bio::DB::GenBank.pm. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="nv" style="color: #008080;">$expected_lengths</span><span class="p">{</span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">},</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">Check contig: get_Seq_by_acc</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">display_id</span><span class="p">;</span></span>
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126
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="perl"><span class="p">}</span></span>
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127
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="perl"></span>
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128
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="perl"><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span></span>
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129
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="perl"></span>
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130
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># bug 1405</span></span>
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131
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@result</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">Fasta</span><span class="p">',</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq_start</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq_stop</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">7</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">Fasta</span><span class="p">',</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq_start</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq_stop</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">7</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_acc</span><span class="p">("</span><span class="s2" style="color: #d14;">A11111</span><span class="p">");};</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">15</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">15</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$seq</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">length</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># complexity tests</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">fasta</span><span class="p">',</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">complexity</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">fasta</span><span class="p">',</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">complexity</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Stream_by_acc</span><span class="p">("</span><span class="s2" style="color: #d14;">21614549</span><span class="p">");};</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">13</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank tests. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">13</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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142
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">4366</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span> <span class="mi" style="color: #099;">620</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">protein</span><span class="p">');</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Test number is labile (dependent on remote results)</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">@@ -152,9 +162,9 @@ SKIP: {</td>
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152
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Real batch retrieval using epost/efetch</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># these tests may change if integrated further into Bio::DB::Gen*</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Currently only useful for retrieving GI's via get_seq_stream</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="perl"> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="perl"> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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156
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_seq_stream</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">uids</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="mi" style="color: #099;">4887706</span> <span class="p">,</span><span class="mi" style="color: #099;">431229</span><span class="p">,</span> <span class="mi" style="color: #099;">147460</span><span class="p">],</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">mode</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">batch</span><span class="p">');};</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank batchmode epost/efetch tests. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">8</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank batchmode epost/efetch tests. Skipping those tests<span class="idiff left right">: $@</span></span><span class="p">",</span> <span class="mi" style="color: #099;">8</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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158
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">('</span><span class="s1" style="color: #d14;">M59757</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">12611</span> <span class="p">,'</span><span class="s1" style="color: #d14;">X76083</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">3140</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">J01670</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">1593</span><span class="p">);</span></span>
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159
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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160
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#e9878a920144a470d96a07badd950289de96555d"><strong>t/GenPept.t</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,12 +16,21 @@ my %expected_lengths = (</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">2AAA_YEAST</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">635</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">})</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-email</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-delay</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-verbose</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLDEBUG</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$gb</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seqio</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Bio::DB::GenPept</span></span>
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenPept</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenPept</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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25
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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26
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_seq_stream</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">uids</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="mi" style="color: #099;">2981015</span><span class="p">,</span> <span class="mi" style="color: #099;">1621261</span><span class="p">,</span> <span class="mi" style="color: #099;">195055</span><span class="p">],</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">mode</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">batch</span><span class="p">');};</span></span>
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27
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenPept tests. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">8</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,7 +50,7 @@ SKIP: {</td>
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41
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="perl"></span>
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42
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="perl"><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span></span>
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43
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="perl"></span>
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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenPept</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(<span class="idiff left">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">-delay</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenPept</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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45
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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46
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_id</span><span class="p">('</span><span class="s1" style="color: #d14;">195055</span><span class="p">');};</span></span>
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47
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to Genbank with Bio::DB::GenPept.pm. Skipping those tests: $@</span><span class="p">",</span> <span class="mi" style="color: #099;">10</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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<li id="ec7c119f53c9107709a5005c78ceaa939da98aaa">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#ec7c119f53c9107709a5005c78ceaa939da98aaa"><strong>t/Query-Genbank.t</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">@@ -23,17 +23,27 @@ my %expected_lengths = (</td>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$gb</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seqio</span><span class="p">,</span> <span class="nv" style="color: #008080;">$seqin</span><span class="p">,</span> <span class="nv" style="color: #008080;">$query</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">})</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-email</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-delay</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"><span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-verbose</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLDEBUG</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># test query facility</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::Query::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-db</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">nucleotide</span><span class="p">',</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-query</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">Onchocerca volvulus[Organism]</span><span class="p">',</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-mindate</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">2002/1/1</span><span class="p">',</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-maxdate</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">2002/12/31</span><span class="p">'),</span> <span class="p">'</span><span class="s1" style="color: #d14;">Bio::DB::Query::GenBank</span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-maxdate</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">2002/12/31</span><span class="p">',</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">),</span> <span class="p">'</span><span class="s1" style="color: #d14;">Bio::DB::Query::GenBank</span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="perl"> <span class="nv" style="color: #008080;">cmp_ok</span> <span class="nv" style="color: #008080;">$query</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">count</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">></span><span class="p">',</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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33
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$query</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ids</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"> <span class="nv" style="color: #008080;">cmp_ok</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">></span><span class="p">',</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">,</span> <span class="nv" style="color: #008080;">$query</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">count</span><span class="p">;</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(<span class="idiff left">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">-delay</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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37
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Stream_by_query</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">);};</span></span>
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38
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank query tests. Skipping those tests</span><span class="p">",</span> <span class="mi" style="color: #099;">5</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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39
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$done</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" 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="61" 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">@@ -51,13 +61,14 @@ $seq = $seqio = undef;</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="perl"></span>
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52
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># test query facility (again)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="perl"><span class="nv" style="color: #008080;">ok</span> <span class="nv" style="color: #008080;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::Query::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-db</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">nucleotide</span><span class="p">',</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-ids</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="sx" style="color: #d14;">qw(J00522 AF303112 2981014)</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-ids</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="sx" style="color: #d14;">qw(J00522 AF303112 2981014)</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">);</span></span>
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55
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl"><span class="nv" style="color: #008080;">SKIP:</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="perl"> <span class="nv" style="color: #008080;">cmp_ok</span> <span class="nv" style="color: #008080;">$query</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">count</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">></span><span class="p">',</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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57
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$query</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ids</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="perl"> <span class="nv" style="color: #008080;">cmp_ok</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">></span><span class="p">',</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">,</span> <span class="nv" style="color: #008080;">$query</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">count</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="perl"> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(<span class="idiff left">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">-delay</span></span><span class="p"><span class="idiff">'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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61
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span><span class="nv" style="color: #008080;">$seqio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Stream_by_query</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">);};</span></span>
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62
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"> <span class="nv" style="color: #008080;">skip</span> <span class="p">"</span><span class="s2" style="color: #d14;">Couldn't connect to complete GenBank query tests. Skipping those tests: $@</span><span class="p">",</span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">if</span> <span class="vg" style="color: #008080;">$@</span><span class="p">;</span></span>
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63
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$done</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</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">@@ -74,5 +85,6 @@ $seq = $seqio = undef;</td>
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74
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="perl"></span>
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75
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># and yet again, for bug 2133</span></span>
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76
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="perl"><span class="nv" style="color: #008080;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::Query::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-query</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">AF303112</span><span class="p">',</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-ids</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="sx" style="color: #d14;">qw(J00522 AF303112 2981014)</span><span class="p">]);</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">-ids</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="sx" style="color: #d14;">qw(J00522 AF303112 2981014)</span><span class="p">],</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="perl"> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">);</span></span>
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78
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="perl"><span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$query</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">query</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">J00522[PACC]|AF303112[PACC]|2981014[UID]</span><span class="p">';</span></span></pre>
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<li id="48ff9b4488f6ca56e79f22bc26b9048a7458c76b">
<a href="https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/commit/620c940138d1a5d0483014bfd1fbb9388b35b25f#48ff9b4488f6ca56e79f22bc26b9048a7458c76b"><strong>t/Taxonomy.t</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">@@ -7,14 +7,21 @@ use Test::RequiresInternet;</td>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"><span class="nv" style="color: #008080;">use_ok</span><span class="p">('</span><span class="s1" style="color: #d14;">Bio::DB::Taxonomy</span><span class="p">');</span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">params</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">})</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-email</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">BIOPERLEMAIL</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"> <span class="nv" style="color: #008080;">$params</span><span class="p">{'</span><span class="s1" style="color: #d14;">-delay</span><span class="p">'}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">entrez</span><span class="p">');</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">entrez</span><span class="p">'<span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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12
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"> <span class="nv" style="color: #008080;">isa_ok</span> <span class="nv" style="color: #008080;">$db</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">Bio::DB::Taxonomy::entrez</span><span class="p">';</span></span>
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13
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"> <span class="nv" style="color: #008080;">isa_ok</span> <span class="nv" style="color: #008080;">$db</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">Bio::DB::Taxonomy</span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="p">}</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="perl"></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">entrez</span><span class="p">');</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">entrez</span><span class="p">'<span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$id</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$n</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,7 +113,6 @@ use_ok('Bio::DB::Taxonomy');</td>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="perl"></span>
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107
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="perl"> <span class="nv" style="color: #008080;">@ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$db</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_taxonids</span><span class="p">('</span><span class="s1" style="color: #d14;">Rhodotorula</span><span class="p">');</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="perl"> <span class="nv" style="color: #008080;">cmp_ok</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">>=</span><span class="p">'</span> <span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="perl"> <span class="nv" style="color: #008080;">diag</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># From NCBI: Taxid 592558 was merged into taxid 5533 on June 16, 2017</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"> <span class="nv" style="color: #008080;">is</span><span class="p">(</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">592558</span> <span class="p">}</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">'</span><span class="s1" style="color: #d14;">Value no longer found</span><span class="p">');</span></span>
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112
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"> <span class="nv" style="color: #008080;">ok</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5533</span> <span class="p">}</span> <span class="nv" style="color: #008080;">@ids</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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">@@ -115,7 +121,7 @@ use_ok('Bio::DB::Taxonomy');</td>
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115
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"></span>
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116
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># we can recursively fetch all descendents of a taxon</span></span>
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117
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="perl"><span class="p">{</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">entrez</span><span class="p">");</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">entrez</span><span class="p">"<span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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119
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="perl"> <span class="nv" style="color: #008080;">$db</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_taxon</span><span class="p">(</span><span class="mi" style="color: #099;">10090</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="perl"></span>
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121
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$lca</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$db</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_taxon</span><span class="p">(</span><span class="mi" style="color: #099;">314146</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,7 +132,7 @@ use_ok('Bio::DB::Taxonomy');</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># tests for #182</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">entrez</span><span class="p">");</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">entrez</span><span class="p">"<span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@taxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qw(viruses Deltavirus unclassified plasmid)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" 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="157" 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">@@ -151,7 +157,7 @@ use_ok('Bio::DB::Taxonomy');</td>
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151
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># tests for #212</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">entrez</span><span class="p">"</span><span class="idiff left right"> </span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$db</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">Taxonomy</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">(</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">source</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">"</span><span class="s2" style="color: #d14;">entrez</span><span class="p">"<span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="nv" style="color: #008080;"><span class="idiff right">params</span></span><span class="p">);</span></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># String | What I expect | What I get</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># ---------------------- | ------------- | ----------</span></span>
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