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+++ b/docs/scripts/html/code/InfoSequenceFiles.html	Wed Jan 20 09:23:18 2016 -0500
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+<html>
+<head>
+<title>MayaChemTools:Code:InfoSequenceFiles.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>
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+<br/>
+<pre>
+   1 #!/usr/bin/perl -w
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: InfoSequenceFiles.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
+   5 <span class="c"># $Revision: 1.29 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$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 <span class="k">use</span> <span class="w">StatisticsUtil</span><span class="sc">;</span>
+  39 
+  40 <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>
+  41 
+  42 <span class="c"># Autoflush STDOUT</span>
+  43 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+  44 
+  45 <span class="c"># Starting message...</span>
+  46 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+  47 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+  48 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  49 
+  50 <span class="c"># Get the options and setup script...</span>
+  51 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  52 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
+  53   <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>
+  54 <span class="s">}</span>
+  55 
+  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="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  62 
+  63 <span class="k">print</span> <span class="q">&quot;Checking input sequence file(s)...\n&quot;</span><span class="sc">;</span>
+  64 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span>
+  65 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  66 
+  67 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  68 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  69   <span class="k">print</span> <span class="q">&quot;\nProcessing sequence files...\n&quot;</span><span class="sc">;</span>
+  70 <span class="s">}</span>
+  71 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
+  72   <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
+  73     <span class="k">print</span> <span class="q">&quot;\nProcessing file $SequenceFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+  74     <span class="i">ListSequenceFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+  75   <span class="s">}</span>
+  76 <span class="s">}</span>
+  77 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  78 
+  79 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  80 
+  81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  82 <span class="i">$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>
+  83 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  84 
+  85 <span class="c">###############################################################################</span>
+  86 
+  87 <span class="c"># List appropriate information...</span>
+<a name="ListSequenceFileInfo-"></a>  88 <span class="k">sub </span><span class="m">ListSequenceFileInfo</span> <span class="s">{</span>
+  89   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  90   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+  91 
+  92   <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+  93 
+  94   <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
+  95 
+  96   <span class="k">my</span><span class="s">(</span><span class="i">$SequencesCount</span><span class="s">)</span> = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Count</span>}<span class="sc">;</span>
+  97   <span class="k">print</span> <span class="q">&quot;\nNumber of sequences: $SequencesCount\n&quot;</span><span class="sc">;</span>
+  98 
+  99   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListShortestSequence</span>} &amp;&amp; <span class="s">(</span><span class="i">$SequencesCount</span> &gt; <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 100     <span class="k">my</span><span class="s">(</span><span class="i">$ShortestSeqID</span><span class="cm">,</span> <span class="i">$ShortestSeq</span><span class="cm">,</span> <span class="i">$ShortestSeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="i">GetShortestSequence</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
+ 101     <span class="k">print</span> <span class="q">&quot;\nShortest sequence information:\nID: $ShortestSeqID; Length:$ShortestSeqLen\n&quot;</span><span class="sc">;</span>
+ 102     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 103       <span class="k">print</span> <span class="q">&quot;Description: $Description\n&quot;</span><span class="sc">;</span>
+ 104     <span class="s">}</span>
+ 105     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
+ 106       <span class="k">print</span> <span class="q">&quot;Sequence: $ShortestSeq\n&quot;</span><span class="sc">;</span>
+ 107     <span class="s">}</span>
+ 108   <span class="s">}</span>
+ 109   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListLongestSequence</span>} &amp;&amp; <span class="s">(</span><span class="i">$SequencesCount</span> &gt; <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 110     <span class="k">my</span><span class="s">(</span><span class="i">$LongestSeqID</span><span class="cm">,</span> <span class="i">$LongestSeq</span><span class="cm">,</span> <span class="i">$LongestSeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="i">GetLongestSequence</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
+ 111     <span class="k">print</span> <span class="q">&quot;\nLongest sequence information:\nID: $LongestSeqID; Length: $LongestSeqLen\n&quot;</span><span class="sc">;</span>
+ 112     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 113       <span class="k">print</span> <span class="q">&quot;Description: $Description\n&quot;</span><span class="sc">;</span>
+ 114     <span class="s">}</span>
+ 115     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
+ 116       <span class="k">print</span> <span class="q">&quot;Sequence: $LongestSeq\n&quot;</span><span class="sc">;</span>
+ 117     <span class="s">}</span>
+ 118   <span class="s">}</span>
+ 119   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FrequencyAnalysis</span>} &amp;&amp; <span class="s">(</span><span class="i">$SequencesCount</span> &gt; <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 120     <span class="i">PerformLengthFrequencyAnalysis</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 121   <span class="s">}</span>
+ 122   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListSequenceLengths</span>}<span class="s">)</span> <span class="s">{</span>
+ 123     <span class="i">ListSequenceLengths</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
+ 124   <span class="s">}</span>
+ 125 
+ 126   <span class="c"># File size and modification information...</span>
+ 127   <span class="k">print</span> <span class="q">&quot;\nFile size: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
+ 128   <span class="k">print</span> <span class="q">&quot;Last modified: &quot;</span><span class="cm">,</span> <span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">&quot; \n&quot;</span><span class="sc">;</span>
+ 129 <span class="s">}</span>
+ 130 
+ 131 <span class="c"># List information about sequence lengths...</span>
+<a name="ListSequenceLengths-"></a> 132 <span class="k">sub </span><span class="m">ListSequenceLengths</span> <span class="s">{</span>
+ 133   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 134   <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span><span class="sc">;</span>
+ 135 
+ 136   <span class="k">print</span> <span class="q">&quot;\nSequence lengths information:\n&quot;</span><span class="sc">;</span>
+ 137   <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>-&gt;{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 138     <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 139     <span class="i">$Description</span> = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 140     <span class="i">$SeqLen</span> = <span class="i">GetSequenceLength</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
+ 141     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span>
+ 142       <span class="i">$Sequence</span> = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span>
+ 143     <span class="s">}</span>
+ 144     <span class="k">print</span> <span class="q">&quot;ID: $ID; Length:$SeqLen\n&quot;</span><span class="sc">;</span>
+ 145     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 146       <span class="k">print</span> <span class="q">&quot;Description: $Description\n&quot;</span><span class="sc">;</span>
+ 147     <span class="s">}</span>
+ 148     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
+ 149       <span class="k">print</span> <span class="q">&quot;Sequence: $Sequence\n&quot;</span><span class="sc">;</span>
+ 150     <span class="s">}</span>
+ 151     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 152       <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+ 153     <span class="s">}</span>
+ 154   <span class="s">}</span>
+ 155 <span class="s">}</span>
+ 156 
+ 157 <span class="c"># Total size of all the fiels...</span>
+<a name="ListTotalSizeOfFiles-"></a> 158 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span>
+ 159   <span class="k">my</span><span class="s">(</span><span class="i">$FileOkayCount</span><span class="cm">,</span> <span class="i">$TotalSize</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
+ 160 
+ 161   <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span>
+ 162   <span class="i">$TotalSize</span> = <span class="n">0</span><span class="sc">;</span>
+ 163 
+ 164   <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
+ 165     <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
+ 166       <span class="i">$FileOkayCount</span>++<span class="sc">;</span>
+ 167       <span class="i">$TotalSize</span> += <span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+ 168     <span class="s">}</span>
+ 169   <span class="s">}</span>
+ 170   <span class="k">if</span> <span class="s">(</span><span class="i">$FileOkayCount</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+ 171     <span class="k">print</span> <span class="q">&quot;\nTotal size of $FileOkayCount files: &quot;</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+ 172   <span class="s">}</span>
+ 173 <span class="s">}</span>
+ 174 
+ 175 
+ 176 <span class="c"># Perform frequency analysis of sequence lengths</span>
+<a name="PerformLengthFrequencyAnalysis-"></a> 177 <span class="k">sub </span><span class="m">PerformLengthFrequencyAnalysis</span> <span class="s">{</span>
+ 178   <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$SequenceLengthsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 179   <span class="k">my</span> <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SequenceLenBin</span><span class="cm">,</span> <span class="i">$LenBin</span><span class="cm">,</span> <span class="i">$SequenceLenCount</span><span class="cm">,</span> <span class="i">@SequenceLengths</span><span class="cm">,</span> <span class="i">%SequenceLenFrequency</span><span class="s">)</span><span class="sc">;</span>
+ 180 
+ 181   <span class="i">@SequenceLengths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 182   <span class="i">%SequenceLenFrequency</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 183   <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>
+ 184     <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>-&gt;{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
+ 185     <span class="i">$SeqLen</span> = <span class="i">GetSequenceLength</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
+ 186     <span class="k">push</span> <span class="i">@SequenceLengths</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="sc">;</span>
+ 187   <span class="s">}</span>
+ 188   <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}}<span class="s">)</span> <span class="s">{</span>
+ 189     <span class="i">%SequenceLenFrequency</span> = <span class="i">Frequency</span><span class="s">(</span>\<span class="i">@SequenceLengths</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}}<span class="s">)</span><span class="sc">;</span>
+ 190   <span class="s">}</span>
+ 191   <span class="k">else</span> <span class="s">{</span>
+ 192     <span class="i">%SequenceLenFrequency</span> = <span class="i">Frequency</span><span class="s">(</span>\<span class="i">@SequenceLengths</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>}<span class="s">)</span><span class="sc">;</span>
+ 193   <span class="s">}</span>
+ 194   <span class="k">print</span> <span class="q">&quot;\nDistribution of sequence lengths (LengthBin =&gt; Count):\n&quot;</span><span class="sc">;</span>
+ 195   <span class="k">for</span> <span class="i">$SequenceLenBin</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%SequenceLenFrequency</span><span class="s">)</span> <span class="s">{</span>
+ 196     <span class="i">$SequenceLenCount</span> = <span class="i">$SequenceLenFrequency</span>{<span class="i">$SequenceLenBin</span>}<span class="sc">;</span>
+ 197     <span class="i">$LenBin</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.1f&quot;</span><span class="cm">,</span> <span class="i">$SequenceLenBin</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+ 198     <span class="k">print</span> <span class="q">&quot;$LenBin =&gt; $SequenceLenCount; &quot;</span><span class="sc">;</span>
+ 199   <span class="s">}</span>
+ 200   <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+ 201 <span class="s">}</span>
+ 202 
+ 203 <span class="c"># Retrieve information about sequence files...</span>
+<a name="RetrieveSequenceFilesInfo-"></a> 204 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span>
+ 205   <span class="k">my</span><span class="s">(</span><span class="i">$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">$FileFormat</span><span class="cm">,</span> <span class="i">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span><span class="sc">;</span>
+ 206 
+ 207   <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 208   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 209   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileFormat</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 210   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 211   <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 212 
+ 213   <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
+ 214     <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 215 
+ 216     <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>
+ 217       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
+ 218       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 219     <span class="s">}</span>
+ 220     <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
+ 221 
+ 222     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 223     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileFormat</span>}[<span class="i">$Index</span>] = <span class="q">&#39;NotSupported&#39;</span><span class="sc">;</span>
+ 224     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
+ 225     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 226 
+ 227     <span class="s">(</span><span class="i">$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>
+ 228     <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span>
+ 229       <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n&quot;</span><span class="sc">;</span>
+ 230       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+ 231     <span class="s">}</span>
+ 232 
+ 233     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
+ 234     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileFormat</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span>
+ 235     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="i">FileSize</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
+ 236 
+ 237     <span class="s">(</span><span class="i">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span> = <span class="i">FormattedFileModificationTimeAndDate</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
+ 238     <span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">&quot;$ModifiedTimeString; $ModifiedDateString&quot;</span><span class="sc">;</span>
+ 239   <span class="s">}</span>
+ 240 <span class="s">}</span>
+ 241 
+ 242 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 243 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 244 
+ 245   <span class="i">$OptionsInfo</span>{<span class="w">All</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">all</span>} ? <span class="i">$Options</span>{<span class="w">all</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 246 
+ 247   <span class="i">$OptionsInfo</span>{<span class="w">Count</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">count</span>} ? <span class="i">$Options</span>{<span class="w">count</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 248   <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
+ 249   <span class="i">$OptionsInfo</span>{<span class="w">Frequency</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">frequency</span>} ? <span class="i">$Options</span>{<span class="w">frequency</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 250   <span class="i">$OptionsInfo</span>{<span class="w">FrequencyBins</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">frequencybins</span>} ? <span class="i">$Options</span>{<span class="w">frequencybins</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 251   <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">ignoregaps</span>} ? <span class="i">$Options</span>{<span class="w">ignoregaps</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 252   <span class="i">$OptionsInfo</span>{<span class="w">Longest</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">longest</span>} ? <span class="i">$Options</span>{<span class="w">longest</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 253   <span class="i">$OptionsInfo</span>{<span class="w">Shortest</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">shortest</span>} ? <span class="i">$Options</span>{<span class="w">shortest</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 254   <span class="i">$OptionsInfo</span>{<span class="w">SequenceLengths</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">sequencelengths</span>} ? <span class="i">$Options</span>{<span class="w">sequencelengths</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 255 
+ 256   <span class="i">$OptionsInfo</span>{<span class="w">FrequencyAnalysis</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">frequency</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 257   <span class="i">$OptionsInfo</span>{<span class="w">ListLongestSequence</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">longest</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 258   <span class="i">$OptionsInfo</span>{<span class="w">ListShortestSequence</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">shortest</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 259   <span class="i">$OptionsInfo</span>{<span class="w">ListSequenceLengths</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">sequencelengths</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 260   <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} =~ <span class="q">/Yes/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 261 
+ 262   <span class="c"># Setup frequency bin values...</span>
+ 263   <span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>} = <span class="n">4</span><span class="sc">;</span>
+ 264   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 265 
+ 266   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">frequencybins</span>} =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span>
+ 267     <span class="k">my</span><span class="s">(</span><span class="i">$BinValue</span><span class="cm">,</span> <span class="i">@SpecifiedBinRange</span><span class="s">)</span><span class="sc">;</span>
+ 268     <span class="i">@SpecifiedBinRange</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span>  <span class="i">$Options</span>{<span class="w">frequencybins</span>}<span class="sc">;</span>
+ 269     <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedBinRange</span> &lt; <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 270       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{frequencybins}, for option \&quot;--frequencybins\&quot; is not valid: Must contain at least two values. \n&quot;</span><span class="sc">;</span>
+ 271     <span class="s">}</span>
+ 272     <span class="k">for</span> <span class="i">$BinValue</span> <span class="s">(</span><span class="i">@SpecifiedBinRange</span><span class="s">)</span> <span class="s">{</span>
+ 273       <span class="k">if</span> <span class="s">(</span>!<span class="i">IsNumerical</span><span class="s">(</span><span class="i">$BinValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 274         <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{frequencybins}, for option \&quot;--frequencybins\&quot; is not valid: Contains non numeric values. \n&quot;</span><span class="sc">;</span>
+ 275       <span class="s">}</span>
+ 276     <span class="s">}</span>
+ 277     <span class="k">my</span><span class="s">(</span><span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="s">)</span><span class="sc">;</span>
+ 278     <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SpecifiedBinRange</span><span class="s">)</span> <span class="s">{</span>
+ 279       <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#SpecifiedBinRange</span><span class="s">)</span> <span class="s">{</span>
+ 280         <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedBinRange</span>[<span class="i">$Index1</span>] &gt;= <span class="i">$SpecifiedBinRange</span>[<span class="i">$Index2</span>]<span class="s">)</span> <span class="s">{</span>
+ 281           <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{frequencybins}, for option \&quot;--frequencybins\&quot; is not valid: Must contain values in ascending order. \n&quot;</span><span class="sc">;</span>
+ 282         <span class="s">}</span>
+ 283       <span class="s">}</span>
+ 284     <span class="s">}</span>
+ 285     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}}<span class="cm">,</span> <span class="i">@SpecifiedBinRange</span><span class="sc">;</span>
+ 286   <span class="s">}</span>
+ 287   <span class="k">else</span> <span class="s">{</span>
+ 288     <span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>} = <span class="i">$Options</span>{<span class="w">frequencybins</span>}<span class="sc">;</span>
+ 289     <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 290       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{frequencybins}, for option \&quot;--frequencybins\&quot; is not valid. Allowed values: positive integer or \&quot;number,number,[number]...\&quot;. \n&quot;</span><span class="sc">;</span>
+ 291     <span class="s">}</span>
+ 292   <span class="s">}</span>
+ 293 <span class="s">}</span>
+ 294 
+ 295 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 296 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 297 
+ 298   <span class="c"># Retrieve all the options...</span>
+ 299   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 300   <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
+ 301   <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">&#39;no&#39;</span><span class="sc">;</span>
+ 302   <span class="i">$Options</span>{<span class="w">frequencybins</span>} = <span class="n">10</span><span class="sc">;</span>
+ 303 
+ 304   <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;all|a&quot;</span><span class="cm">,</span> <span class="q">&quot;count|c&quot;</span><span class="cm">,</span> <span class="q">&quot;detail|d=i&quot;</span><span class="cm">,</span> <span class="q">&quot;frequency|f&quot;</span><span class="cm">,</span> <span class="q">&quot;frequencybins=s&quot;</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;longest|l&quot;</span><span class="cm">,</span> <span class="q">&quot;shortest|s&quot;</span><span class="cm">,</span> <span class="q">&quot;sequencelengths&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>
+ 305     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 306   <span class="s">}</span>
+ 307   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 308     <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>
+ 309       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 310     <span class="s">}</span>
+ 311     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+ 312   <span class="s">}</span>
+ 313   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 314     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d --detail\&quot; is not valid. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
+ 315   <span class="s">}</span>
+ 316   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 317     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{ignoregaps}, for option \&quot;-i --IgnoreGaps\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+ 318   <span class="s">}</span>
+ 319 <span class="s">}</span>
+ 320 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>