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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> </center> <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 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</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">$0</span><span class="s">)</span><span class="sc">;</span> 47 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</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> < <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">"$FindBin::Bin/$ScriptName"</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">"aln msf fasta fta pir"</span><span class="s">)</span><span class="sc">;</span> 58 59 <span class="k">print</span> <span class="q">"Processing options...\n"</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">"Checking input sequence file(s)...\n"</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">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 68 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 69 <span class="k">print</span> <span class="q">"\nProcessing sequence files...\n"</span><span class="sc">;</span> 70 <span class="s">}</span> 71 <span class="k">for</span> <span class="i">$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">"\nProcessing file $SequenceFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 74 <span class="i">ListSequenceFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 75 <span class="s">}</span> 76 <span class="s">}</span> 77 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 78 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</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">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 84 85 <span class="c">###############################################################################</span> 86 87 <span class="c"># List appropriate information...</span> <a name="ListSequenceFileInfo-"></a> 88 <span class="k">sub </span><span class="m">ListSequenceFileInfo</span> <span class="s">{</span> 89 <span class="k">my</span><span class="s">(</span><span class="i">$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>->{<span class="w">Count</span>}<span class="sc">;</span> 97 <span class="k">print</span> <span class="q">"\nNumber of sequences: $SequencesCount\n"</span><span class="sc">;</span> 98 99 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListShortestSequence</span>} && <span class="s">(</span><span class="i">$SequencesCount</span> > <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 100 <span class="k">my</span><span class="s">(</span><span class="i">$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">"\nShortest sequence information:\nID: $ShortestSeqID; Length:$ShortestSeqLen\n"</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>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 103 <span class="k">print</span> <span class="q">"Description: $Description\n"</span><span class="sc">;</span> 104 <span class="s">}</span> 105 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span> 106 <span class="k">print</span> <span class="q">"Sequence: $ShortestSeq\n"</span><span class="sc">;</span> 107 <span class="s">}</span> 108 <span class="s">}</span> 109 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListLongestSequence</span>} && <span class="s">(</span><span class="i">$SequencesCount</span> > <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 110 <span class="k">my</span><span class="s">(</span><span class="i">$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">"\nLongest sequence information:\nID: $LongestSeqID; Length: $LongestSeqLen\n"</span><span class="sc">;</span> 112 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 113 <span class="k">print</span> <span class="q">"Description: $Description\n"</span><span class="sc">;</span> 114 <span class="s">}</span> 115 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span> 116 <span class="k">print</span> <span class="q">"Sequence: $LongestSeq\n"</span><span class="sc">;</span> 117 <span class="s">}</span> 118 <span class="s">}</span> 119 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FrequencyAnalysis</span>} && <span class="s">(</span><span class="i">$SequencesCount</span> > <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 120 <span class="i">PerformLengthFrequencyAnalysis</span><span class="s">(</span><span class="i">$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">"\nFile size: "</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">" \n"</span><span class="sc">;</span> 128 <span class="k">print</span> <span class="q">"Last modified: "</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">" \n"</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">$Description</span><span class="s">)</span><span class="sc">;</span> 135 136 <span class="k">print</span> <span class="q">"\nSequence lengths information:\n"</span><span class="sc">;</span> 137 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> 138 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 139 <span class="i">$Description</span> = <span class="i">$SequenceDataRef</span>->{<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">"ID: $ID; Length:$SeqLen\n"</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>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 146 <span class="k">print</span> <span class="q">"Description: $Description\n"</span><span class="sc">;</span> 147 <span class="s">}</span> 148 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span> 149 <span class="k">print</span> <span class="q">"Sequence: $Sequence\n"</span><span class="sc">;</span> 150 <span class="s">}</span> 151 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 152 <span class="k">print</span> <span class="q">"\n"</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> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 171 <span class="k">print</span> <span class="q">"\nTotal size of $FileOkayCount files: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</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>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> 184 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<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">"\nDistribution of sequence lengths (LengthBin => Count):\n"</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> <=> <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">$LenBin</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.1f"</span><span class="cm">,</span> <span class="i">$SequenceLenBin</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> 198 <span class="k">print</span> <span class="q">"$LenBin => $SequenceLenCount; "</span><span class="sc">;</span> 199 <span class="s">}</span> 200 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span> 201 <span class="s">}</span> 202 203 <span class="c"># Retrieve information about sequence files...</span> <a name="RetrieveSequenceFilesInfo-"></a> 204 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span> 205 <span class="k">my</span><span class="s">(</span><span class="i">$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">"$SequenceFile"</span><span class="s">)</span> <span class="s">{</span> 217 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 218 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 219 <span class="s">}</span> 220 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> 221 222 <span class="i">$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">$Index</span>] = <span class="q">'NotSupported'</span><span class="sc">;</span> 224 <span class="i">$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">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 226 227 <span class="s">(</span><span class="i">$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">"Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n"</span><span class="sc">;</span> 230 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 231 <span class="s">}</span> 232 233 <span class="i">$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">"$ModifiedTimeString; $ModifiedDateString"</span><span class="sc">;</span> 239 <span class="s">}</span> 240 <span class="s">}</span> 241 242 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 243 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 244 245 <span class="i">$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> < <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 270 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain at least two values. \n"</span><span class="sc">;</span> 271 <span class="s">}</span> 272 <span class="k">for</span> <span class="i">$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">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Contains non numeric values. \n"</span><span class="sc">;</span> 275 <span class="s">}</span> 276 <span class="s">}</span> 277 <span class="k">my</span><span class="s">(</span><span class="i">$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>] >= <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">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain values in ascending order. \n"</span><span class="sc">;</span> 282 <span class="s">}</span> 283 <span class="s">}</span> 284 <span class="s">}</span> 285 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid. Allowed values: positive integer or \"number,number,[number]...\". \n"</span><span class="sc">;</span> 291 <span class="s">}</span> 292 <span class="s">}</span> 293 <span class="s">}</span> 294 295 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 296 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 297 298 <span class="c"># Retrieve all the options...</span> 299 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 300 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span> 301 <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">'no'</span><span class="sc">;</span> 302 <span class="i">$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">"all|a"</span><span class="cm">,</span> <span class="q">"count|c"</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"frequency|f"</span><span class="cm">,</span> <span class="q">"frequencybins=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"ignoregaps|i=s"</span><span class="cm">,</span> <span class="q">"longest|l"</span><span class="cm">,</span> <span class="q">"shortest|s"</span><span class="cm">,</span> <span class="q">"sequencelengths"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 305 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 306 <span class="s">}</span> 307 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 310 <span class="s">}</span> 311 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> 312 <span class="s">}</span> 313 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n"</span><span class="sc">;</span> 315 <span class="s">}</span> 316 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{ignoregaps}, for option \"-i --IgnoreGaps\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> 318 <span class="s">}</span> 319 <span class="s">}</span> 320 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>