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+<html>
+<head>
+<title>MayaChemTools:Code:ExtractFromSequenceFiles.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
+</head>
+<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
+</center>
+<br/>
+<pre>
+   1 #!/usr/bin/perl -w
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: ExtractFromSequenceFiles.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
+   5 <span class="c"># $Revision: 1.23 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
+  37 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span>
+  38 
+  39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
+  40 
+  41 <span class="c"># Autoflush STDOUT</span>
+  42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+  43 
+  44 <span class="c"># Starting message...</span>
+  45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+  46 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+  47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  48 
+  49 <span class="c"># Setup script usage message...</span>
+  50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  52   <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
+  53 <span class="s">}</span>
+  54 
+  55 <span class="c"># Expand wild card file names...</span>
+  56 <span class="k">my</span><span class="s">(</span><span class="i">@SequenceFilesList</span><span class="s">)</span><span class="sc">;</span>
+  57 <span class="i">@SequenceFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">&quot;aln msf fasta fta pir&quot;</span><span class="s">)</span><span class="sc">;</span>
+  58 
+  59 <span class="c"># Process options...</span>
+  60 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  61 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  62 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  63 
+  64 <span class="c"># Set up information about input files...</span>
+  65 <span class="k">print</span> <span class="q">&quot;Checking input sequence file(s)...\n&quot;</span><span class="sc">;</span>
+  66 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+  67 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  68 
+  69 <span class="c"># Process input files..</span>
+  70 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  71 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  72   <span class="k">print</span> <span class="q">&quot;\nProcessing sequence files...\n&quot;</span><span class="sc">;</span>
+  73 <span class="s">}</span>
+  74 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
+  75   <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+  76     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SequenceFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+  77     <span class="i">ExtractFromSequenceFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  78   <span class="s">}</span>
+  79 <span class="s">}</span>
+  80 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  81 
+  82 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  83 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
+  84 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  85 
+  86 <span class="c">###############################################################################</span>
+  87 
+  88 <span class="c"># Extract from sequence files...</span>
+<a name="ExtractFromSequenceFiles-"></a>  89 <span class="k">sub </span><span class="m">ExtractFromSequenceFiles</span> <span class="s">{</span>
+  90   <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  91   <span class="k">my</span><span class="s">(</span><span class="i">$OutSequenceFile</span><span class="cm">,</span> <span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+  92 
+  93   <span class="c"># Read sequence file...</span>
+  94   <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+  95   <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">&quot;$SequenceFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $SequenceFile: $! \n&quot;</span><span class="sc">;</span>
+  96   <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
+  97   <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
+  98 
+  99   <span class="i">$OutSequenceFile</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
+ 100   <span class="k">print</span> <span class="q">&quot;Generating sequence file $OutSequenceFile...\n&quot;</span><span class="sc">;</span>
+ 101 
+ 102   <span class="c"># Retrieve sequence data for specified sequences...</span>
+ 103   <span class="i">$SpecifiedSequenceDataRef</span> = <span class="i">GetSpecifiedSequenceData</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 104 
+ 105   <span class="c"># Handle gaps...</span>
+ 106   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span>
+ 107     <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">IDs</span>}} &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+ 108       <span class="k">if</span> <span class="s">(</span><span class="i">AreSequenceLengthsIdentical</span><span class="s">(</span><span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 109         <span class="i">$SpecifiedSequenceDataRef</span> = <span class="i">RemoveSequenceAlignmentGapColumns</span><span class="s">(</span><span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 110       <span class="s">}</span>
+ 111     <span class="s">}</span>
+ 112     <span class="k">else</span> <span class="s">{</span>
+ 113       <span class="c"># Remove the gaps from the sequence...</span>
+ 114       <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span>
+ 115       <span class="i">$ID</span> = <span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span>
+ 116       <span class="i">$Sequence</span> = <span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 117       <span class="i">$SpecifiedSequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span>
+ 118     <span class="s">}</span>
+ 119   <span class="s">}</span>
+ 120 
+ 121   <span class="c"># Write out the file...</span>
+ 122   <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$OutSequenceFile</span><span class="cm">,</span> <span class="i">$SpecifiedSequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span>
+ 123 <span class="s">}</span>
+ 124 
+ 125 <span class="c"># Get specified sequence data...</span>
+<a name="GetSpecifiedSequenceData-"></a> 126 <span class="k">sub </span><span class="m">GetSpecifiedSequenceData</span> <span class="s">{</span>
+ 127   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 128 
+ 129   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span>
+ 130     <span class="k">return</span> <span class="i">GetDataBySequenceIDs</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 131   <span class="s">}</span>
+ 132   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span>
+ 133     <span class="k">return</span> <span class="i">GetDataBySequenceNums</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 134   <span class="s">}</span>
+ 135   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span>
+ 136     <span class="k">return</span> <span class="i">GetDataBySequenceNumRange</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 137   <span class="s">}</span>
+ 138   <span class="k">else</span> <span class="s">{</span>
+ 139     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 140   <span class="s">}</span>
+ 141 <span class="s">}</span>
+ 142 
+ 143 <span class="c"># Get specified sequence data...</span>
+<a name="GetDataBySequenceIDs-"></a> 144 <span class="k">sub </span><span class="m">GetDataBySequenceIDs</span> <span class="s">{</span>
+ 145   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 146   <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">$IDMatched</span><span class="cm">,</span> <span class="i">$SpecifiedID</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span>
+ 147 
+ 148   <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span>
+ 149   <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 150   <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 151   <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 152   <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 153 
+ 154   <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 155   <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>-&gt;{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 156     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">MatchExactSequenceIDs</span>}<span class="s">)</span> <span class="s">{</span>
+ 157       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$ID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+ 158         <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
+ 159       <span class="s">}</span>
+ 160       <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceCount</span> &gt;= <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 161         <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span>
+ 162       <span class="s">}</span>
+ 163       <span class="i">$SequenceCount</span>++<span class="sc">;</span>
+ 164     <span class="s">}</span>
+ 165     <span class="k">else</span> <span class="s">{</span>
+ 166       <span class="c"># Does this ID contains specified ID as substring...</span>
+ 167       <span class="i">$IDMatched</span> = <span class="n">0</span><span class="sc">;</span>
+ 168       <span class="j">SPECIFIEDID:</span> <span class="k">for</span> <span class="i">$SpecifiedID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 169         <span class="k">if</span> <span class="s">(</span><span class="i">$ID</span> =~ <span class="q">/$SpecifiedID/i</span><span class="s">)</span> <span class="s">{</span>
+ 170           <span class="i">$IDMatched</span> = <span class="n">1</span><span class="sc">;</span>
+ 171           <span class="k">last</span> <span class="j">SPECIFIEDID</span><span class="sc">;</span>
+ 172         <span class="s">}</span>
+ 173       <span class="s">}</span>
+ 174       <span class="k">if</span> <span class="s">(</span>!<span class="i">$IDMatched</span><span class="s">)</span> <span class="s">{</span>
+ 175         <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
+ 176       <span class="s">}</span>
+ 177       <span class="i">$SequenceCount</span>++<span class="sc">;</span>
+ 178     <span class="s">}</span>
+ 179     <span class="c"># Collect sequence data...</span>
+ 180     <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span>
+ 181     <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 182     <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 183   <span class="s">}</span>
+ 184 
+ 185   <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span>
+ 186 <span class="s">}</span>
+ 187 
+ 188 <span class="c"># Get specified sequence data...</span>
+<a name="GetDataBySequenceNums-"></a> 189 <span class="k">sub </span><span class="m">GetDataBySequenceNums</span> <span class="s">{</span>
+ 190   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 191   <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceNum</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span>
+ 192 
+ 193   <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span>
+ 194   <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 195   <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 196   <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 197   <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 198 
+ 199   <span class="i">$SequenceNum</span> = <span class="n">0</span><span class="sc">;</span>
+ 200   <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 201   <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>-&gt;{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 202     <span class="i">$SequenceNum</span>++<span class="sc">;</span>
+ 203     <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="i">$SequenceNum</span>}<span class="s">)</span> <span class="s">{</span>
+ 204       <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
+ 205     <span class="s">}</span>
+ 206     <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceCount</span> &gt;= <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 207       <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span>
+ 208     <span class="s">}</span>
+ 209     <span class="i">$SequenceCount</span>++<span class="sc">;</span>
+ 210 
+ 211     <span class="c"># Collect sequence data...</span>
+ 212     <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span>
+ 213     <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 214     <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 215   <span class="s">}</span>
+ 216 
+ 217   <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span>
+ 218 <span class="s">}</span>
+ 219 
+ 220 <span class="c"># Get specified sequence data...</span>
+<a name="GetDataBySequenceNumRange-"></a> 221 <span class="k">sub </span><span class="m">GetDataBySequenceNumRange</span> <span class="s">{</span>
+ 222   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 223   <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceNum</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span>
+ 224 
+ 225   <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span>
+ 226   <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 227   <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 228   <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 229   <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 230 
+ 231   <span class="i">$SequenceNum</span> = <span class="n">0</span><span class="sc">;</span>
+ 232   <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 233   <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>-&gt;{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 234     <span class="i">$SequenceNum</span>++<span class="sc">;</span>
+ 235 
+ 236     <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$SequenceNum</span> &gt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">0</span>] &amp;&amp; <span class="i">$SequenceNum</span> &lt;= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">1</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 237       <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
+ 238     <span class="s">}</span>
+ 239     <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceNum</span> &gt; <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
+ 240       <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span>
+ 241     <span class="s">}</span>
+ 242     <span class="i">$SequenceCount</span>++<span class="sc">;</span>
+ 243     <span class="c"># Collect sequence data...</span>
+ 244     <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span>
+ 245     <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 246     <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 247   <span class="s">}</span>
+ 248 
+ 249   <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span>
+ 250 <span class="s">}</span>
+ 251 
+ 252 
+ 253 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 254 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 255   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 256 
+ 257   <span class="c"># Miscellaneous options...</span>
+ 258   <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} =~ <span class="q">/Yes/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 259 
+ 260   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 261   <span class="i">$OptionsInfo</span>{<span class="w">MatchExactSequenceIDs</span>} = <span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} =~ <span class="q">/Exact/i</span> ? <span class="n">1</span> <span class="co">:</span><span class="n">0</span><span class="sc">;</span>
+ 262 
+ 263   <span class="c"># Check specified sequences value...</span>
+ 264   <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequences</span>} = <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
+ 265   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 266   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 267 
+ 268   <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 269   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span>
+ 270     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span>
+ 271       <span class="k">die</span> <span class="q">&quot;Error: No value specified for option \&quot;-s, --Sequences\&quot; during \&quot;SequenceID\&quot; of \&quot;-m, --mode\&quot; option\n&quot;</span><span class="sc">;</span>
+ 272     <span class="s">}</span>
+ 273     <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
+ 274   <span class="s">}</span>
+ 275   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span>
+ 276     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span>
+ 277       <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
+ 278       <span class="k">my</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="sc">;</span>
+ 279       <span class="k">for</span> <span class="i">$SequenceNum</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span>
+ 280         <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 281           <span class="k">die</span> <span class="q">&quot;Error: The value specified, $SequenceNum, in \&quot;$Options{sequences}\&quot; for option \&quot;-s, --Sequences\&quot; is not valid: Valid values: &gt; 0\n&quot;</span><span class="sc">;</span>
+ 282         <span class="s">}</span>
+ 283       <span class="s">}</span>
+ 284     <span class="s">}</span>
+ 285     <span class="k">else</span> <span class="s">{</span>
+ 286       <span class="k">push</span> <span class="i">@SpecifiedSequenceIDs</span><span class="cm">,</span> <span class="q">&quot;1&quot;</span><span class="sc">;</span>
+ 287     <span class="s">}</span>
+ 288   <span class="s">}</span>
+ 289   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span>
+ 290     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span>
+ 291       <span class="k">die</span> <span class="q">&quot;Error: No value specified for option \&quot;-s, --Sequences\&quot; during \&quot;SequenceNumRange\&quot; of \&quot;-m, --mode\&quot; option\n&quot;</span><span class="sc">;</span>
+ 292     <span class="s">}</span>
+ 293     <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span>
+ 294     <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 295       <span class="k">die</span> <span class="q">&quot;Error: The number of values&quot;</span><span class="cm">,</span> <span class="k">scalar</span> <span class="i">@SpecifiedSequenceIDs</span><span class="cm">,</span> <span class="q">&quot; specified, $Options{sequences}, for option \&quot;-s, --Sequences\&quot; are not valid. Number of values must be 2 to indicate starting and ending sequence number.\n&quot;</span><span class="sc">;</span>
+ 296     <span class="s">}</span>
+ 297     <span class="k">my</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="sc">;</span>
+ 298     <span class="k">for</span> <span class="i">$SequenceNum</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span>
+ 299       <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 300         <span class="k">die</span> <span class="q">&quot;Error: The value specified, $SequenceNum, in \&quot;$Options{sequences}\&quot; for option \&quot;-s, --Sequences\&quot; is not valid: Valid values: &gt; 0\n&quot;</span><span class="sc">;</span>
+ 301       <span class="s">}</span>
+ 302     <span class="s">}</span>
+ 303     <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedSequenceIDs</span>[<span class="n">0</span>] &gt; <span class="i">$SpecifiedSequenceIDs</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span>
+ 304       <span class="k">die</span> <span class="q">&quot;Error: The value specified \&quot;$Options{sequences}\&quot; for option \&quot;-s, --Sequences\&quot; are not valid: Starting sequence number $SpecifiedSequenceIDs[0] must be smaller than ending sequence number $SpecifiedSequenceIDs[1]\n&quot;</span><span class="sc">;</span>
+ 305     <span class="s">}</span>
+ 306   <span class="s">}</span>
+ 307   <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="cm">,</span> <span class="i">@SpecifiedSequenceIDs</span><span class="sc">;</span>
+ 308   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceID</span><span class="s">)</span><span class="sc">;</span>
+ 309   <span class="k">for</span> <span class="i">$SequenceID</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span>
+ 310     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span>
+ 311       <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SequenceID</span><span class="s">)</span>} = <span class="i">$SequenceID</span><span class="sc">;</span>
+ 312     <span class="s">}</span>
+ 313     <span class="k">else</span> <span class="s">{</span>
+ 314       <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceID</span><span class="sc">;</span>
+ 315     <span class="s">}</span>
+ 316   <span class="s">}</span>
+ 317 
+ 318   <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>} = <span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="sc">;</span>
+ 319   <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 320   <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 321 <span class="s">}</span>
+ 322 
+ 323 <span class="c"># Retrieve information about sequence files...</span>
+<a name="RetrieveSequenceFilesInfo-"></a> 324 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span>
+ 325   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$FileSupported</span><span class="cm">,</span> <span class="i">$FileFormat</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="cm">,</span> <span class="i">$OutFileMode</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 326 
+ 327   <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 328   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 329   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 330   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 331   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 332   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 333   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 334 
+ 335   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
+ 336     <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 337     <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 338     <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 339     <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 340     <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 341     <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="q">&#39;NotSupported&#39;</span><span class="sc">;</span>
+ 342     <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 343 
+ 344     <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">&quot;$SequenceFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+ 345       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 346       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 347     <span class="s">}</span>
+ 348     <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
+ 349 
+ 350     <span class="s">(</span><span class="i">$FileSupported</span><span class="cm">,</span> <span class="i">$FileFormat</span><span class="s">)</span> = <span class="i">IsSupportedSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
+ 351     <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span>
+ 352       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n&quot;</span><span class="sc">;</span>
+ 353       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 354     <span class="s">}</span>
+ 355     <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
+ 356 
+ 357     <span class="i">$SequenceCount</span> = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Count</span>}<span class="sc">;</span>
+ 358     <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceCount</span><span class="s">)</span> <span class="s">{</span>
+ 359       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Sequence data is missing.\n&quot;</span><span class="sc">;</span>
+ 360       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 361     <span class="s">}</span>
+ 362 
+ 363     <span class="c"># Setup output file names...</span>
+ 364     <span class="i">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 365     <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
+ 366     <span class="i">$OutFileExt</span> = <span class="q">&#39;fasta&#39;</span><span class="sc">;</span>
+ 367     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SequenceFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 368       <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
+ 369       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+ 370         <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+ 371       <span class="s">}</span>
+ 372       <span class="k">else</span> <span class="s">{</span>
+ 373         <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
+ 374       <span class="s">}</span>
+ 375       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+ 376     <span class="s">}</span>
+ 377     <span class="k">else</span> <span class="s">{</span>
+ 378       <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
+ 379     <span class="s">}</span>
+ 380     <span class="j">MODE:</span> <span class="s">{</span>
+ 381         <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;SequenceID&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+ 382         <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;SequenceNum&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+ 383         <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">&#39;SequenceNumRange&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
+ 384         <span class="i">$OutFileMode</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 385     <span class="s">}</span>
+ 386     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
+ 387       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">&quot;${OutFileRoot}${OutFileMode}.${OutFileExt}&quot;</span><span class="s">)</span> <span class="s">{</span>
+ 388         <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}${OutFileMode}.${OutFileExt} already exists\n&quot;</span><span class="sc">;</span>
+ 389         <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 390       <span class="s">}</span>
+ 391     <span class="s">}</span>
+ 392 
+ 393     <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+ 394     <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
+ 395     <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span>
+ 396     <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">&quot;${OutFileRoot}${OutFileMode}.${OutFileExt}&quot;</span><span class="sc">;</span>
+ 397 
+ 398     <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span>
+ 399     <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="i">$SequenceCount</span><span class="sc">;</span>
+ 400   <span class="s">}</span>
+ 401 <span class="s">}</span>
+ 402 
+ 403 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 404 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 405 
+ 406   <span class="c"># Retrieve all the options...</span>
+ 407   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 408   <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
+ 409   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;SequenceNum&#39;</span><span class="sc">;</span>
+ 410   <span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} = <span class="q">&#39;Relaxed&#39;</span><span class="sc">;</span>
+ 411   <span class="i">$Options</span>{<span class="w">sequencelength</span>} = <span class="n">80</span><span class="sc">;</span>
+ 412 
+ 413   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;ignoregaps|i=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequences|s=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequenceidmatch=s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencelength=i&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 414     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 415   <span class="s">}</span>
+ 416   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 417     <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 418       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 419     <span class="s">}</span>
+ 420     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+ 421   <span class="s">}</span>
+ 422   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 423     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ignoregaps}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+ 424   <span class="s">}</span>
+ 425   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(SequenceID|SequenceNum|SequenceNumRange)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 426     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m --mode\&quot; is not valid. Allowed values: SequenceID, SequenceNum, or SequenceNumRange\n&quot;</span><span class="sc">;</span>
+ 427   <span class="s">}</span>
+ 428   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} !~ <span class="q">/^(Exact|Relaxed)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 429     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{sequenceidmatch}, for option \&quot;--SequenceIDMatch\&quot; is not valid. Allowed values: Exact or Relaxed\n&quot;</span><span class="sc">;</span>
+ 430   <span class="s">}</span>
+ 431   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 432     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{sequencelength}, for option \&quot;--SequenceLength\&quot; is not valid. Allowed values: &gt;0\n&quot;</span><span class="sc">;</span>
+ 433   <span class="s">}</span>
+ 434 <span class="s">}</span>
+ 435 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>