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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/code/AnalyzeSequenceFilesData.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,727 @@ +<html> +<head> +<title>MayaChemTools:Code:AnalyzeSequenceFilesData.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: AnalyzeSequenceFilesData.pl,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:46:04 $</span> + 5 <span class="c"># $Revision: 1.33 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$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">AminoAcids</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">NucleicAcids</span><span class="sc">;</span> + 40 + 41 <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> + 42 + 43 <span class="c"># Autoflush STDOUT</span> + 44 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> + 45 + 46 <span class="c"># Starting message...</span> + 47 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> + 48 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> + 49 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 50 + 51 <span class="c"># Setup script usage message...</span> + 52 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 53 <span class="k">if</span> <span class="s">(</span><span class="i">$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> + 54 <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> + 55 <span class="s">}</span> + 56 + 57 <span class="c"># Expand wild card file names...</span> + 58 <span class="k">my</span><span class="s">(</span><span class="i">@SequenceFilesList</span><span class="s">)</span><span class="sc">;</span> + 59 <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> + 60 + 61 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> + 62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> + 63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 64 + 65 <span class="c"># Set up information about input files...</span> + 66 <span class="k">print</span> <span class="q">"Checking input sequence file(s)...\n"</span><span class="sc">;</span> + 67 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span> + 68 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 69 <span class="i">SetupSequenceRegionsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 70 + 71 <span class="c"># Process input files..</span> + 72 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 73 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 74 <span class="k">print</span> <span class="q">"\nProcessing sequence files...\n"</span><span class="sc">;</span> + 75 <span class="s">}</span> + 76 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span> + 77 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> + 78 <span class="k">print</span> <span class="q">"\nProcessing file $SequenceFilesList[$FileIndex]...\n"</span><span class="sc">;</span> + 79 <span class="i">AnalyzeSequenceFileData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 80 <span class="s">}</span> + 81 <span class="s">}</span> + 82 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> + 83 + 84 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 85 <span class="i">$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> + 86 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 87 + 88 <span class="c">###############################################################################</span> + 89 + 90 <span class="c"># Analyze sequence file...</span> +<a name="AnalyzeSequenceFileData-"></a> 91 <span class="k">sub </span><span class="m">AnalyzeSequenceFileData</span> <span class="s">{</span> + 92 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 93 <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> + 94 + 95 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 96 + 97 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $SequenceFile: $! \n"</span><span class="sc">;</span> + 98 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> + 99 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> + 100 + 101 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculatePercentIdentityMatrix</span>}<span class="s">)</span> <span class="s">{</span> + 102 <span class="i">CalculatePercentIdentityMatrix</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> + 103 <span class="s">}</span> + 104 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span> + 105 <span class="i">PerformResidueFrequencyAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> + 106 <span class="s">}</span> + 107 <span class="s">}</span> + 108 + 109 <span class="c"># Calculate percent identity matrix...</span> +<a name="CalculatePercentIdentityMatrix-"></a> 110 <span class="k">sub </span><span class="m">CalculatePercentIdentityMatrix</span> <span class="s">{</span> + 111 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 112 <span class="k">my</span><span class="s">(</span><span class="i">$PercentIdentity</span><span class="cm">,</span> <span class="i">$PercentIdentityMatrixFile</span><span class="cm">,</span> <span class="i">$PercentIdentityMatrixRef</span><span class="cm">,</span> <span class="i">$RowID</span><span class="cm">,</span> <span class="i">$ColID</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> + 113 + 114 <span class="i">$PercentIdentityMatrixFile</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>] . <span class="q">'PercentIdentityMatrix.'</span> . <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 115 <span class="i">$PercentIdentityMatrixRef</span> = <span class="i">CalculatePercentSequenceIdentityMatrix</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="s">)</span><span class="sc">;</span> + 116 + 117 <span class="k">print</span> <span class="q">"Generating percent identity matrix file $PercentIdentityMatrixFile...\n"</span><span class="sc">;</span> + 118 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PercentIdentityMatrixFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Can't open $PercentIdentityMatrixFile: $!\n"</span><span class="sc">;</span> + 119 + 120 <span class="c"># Write out column labels...</span> + 121 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 122 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span> + 123 <span class="k">for</span> <span class="i">$ColID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> + 124 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ColID</span><span class="sc">;</span> + 125 <span class="s">}</span> + 126 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 127 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 128 + 129 <span class="c"># Write out rows...</span> + 130 <span class="k">for</span> <span class="i">$RowID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> + 131 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 132 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$RowID</span><span class="sc">;</span> + 133 <span class="k">for</span> <span class="i">$ColID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> + 134 <span class="i">$PercentIdentity</span> = <span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">PercentIdentity</span>}{<span class="i">$RowID</span>}{<span class="i">$ColID</span>}<span class="sc">;</span> + 135 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PercentIdentity</span><span class="sc">;</span> + 136 <span class="s">}</span> + 137 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 138 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 139 <span class="s">}</span> + 140 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> + 141 <span class="s">}</span> + 142 + 143 <span class="c"># Perform frequency analysis...</span> +<a name="PerformResidueFrequencyAnalysis-"></a> 144 <span class="k">sub </span><span class="m">PerformResidueFrequencyAnalysis</span> <span class="s">{</span> + 145 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 146 + 147 <span class="i">CountResiduesInRegions</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> + 148 <span class="i">CalculatePercentResidueFrequencyInRegions</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> + 149 <span class="i">GeneratePercentResidueFrequencyOutFilesForRegions</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> + 150 <span class="s">}</span> + 151 + 152 <span class="c"># Count residues...</span> +<a name="CountResiduesInRegions-"></a> 153 <span class="k">sub </span><span class="m">CountResiduesInRegions</span> <span class="s">{</span> + 154 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 155 + 156 <span class="c"># Setup rerfernce sequence data...</span> + 157 <span class="k">my</span><span class="s">(</span><span class="i">$RefereceSequenceID</span><span class="cm">,</span> <span class="i">$RefereceSequence</span><span class="s">)</span><span class="sc">;</span> + 158 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 159 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 160 + 161 <span class="c"># Count residues...</span> + 162 <span class="k">my</span><span class="s">(</span><span class="i">$RegionID</span><span class="cm">,</span> <span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$ResNum</span><span class="cm">,</span> <span class="i">$ResIndex</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$Residue</span><span class="s">)</span><span class="sc">;</span> + 163 <span class="k">for</span> <span class="i">$RegionID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="w">RegionIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 164 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span> + 165 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span> + 166 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> + 167 <span class="i">$ResIndex</span> = <span class="i">$ResNum</span> - <span class="n">1</span><span class="sc">;</span> + 168 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} && <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$FileIndex</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>}<span class="s">)</span> <span class="s">{</span> + 169 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> + 170 <span class="s">}</span> + 171 <span class="c"># Go over residues in column $ResNum in all the sequences...</span> + 172 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> + 173 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> + 174 <span class="i">$Residue</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$ResIndex</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 175 <span class="k">if</span> <span class="s">(</span><span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 176 <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}{<span class="w">Gap</span>} += <span class="n">1</span><span class="sc">;</span> + 177 <span class="s">}</span> + 178 <span class="k">else</span> <span class="s">{</span> + 179 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>}<span class="s">)</span> <span class="s">{</span> + 180 <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>} += <span class="n">1</span><span class="sc">;</span> + 181 <span class="s">}</span> + 182 <span class="k">else</span> <span class="s">{</span> + 183 <span class="c"># Internal error...</span> + 184 <span class="k">print</span> <span class="q">"Warning: Ignoring residue $Residue in sequence $ID during ResidueFrequencyAnalysis calculation: Unknown residue...\n"</span><span class="sc">;</span> + 185 <span class="s">}</span> + 186 <span class="s">}</span> + 187 <span class="s">}</span> + 188 <span class="s">}</span> + 189 <span class="s">}</span> + 190 <span class="s">}</span> + 191 + 192 <span class="c"># Calculate percent frequency for various residues in the sequence regions...</span> +<a name="CalculatePercentResidueFrequencyInRegions-"></a> 193 <span class="k">sub </span><span class="m">CalculatePercentResidueFrequencyInRegions</span> <span class="s">{</span> + 194 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 195 <span class="k">my</span><span class="s">(</span><span class="i">$RegionID</span><span class="cm">,</span> <span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$ResNum</span><span class="cm">,</span> <span class="i">$Residue</span><span class="cm">,</span> <span class="i">$Count</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="cm">,</span> <span class="i">$MaxResiduesCount</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span><span class="sc">;</span> + 196 + 197 <span class="i">$MaxResiduesCount</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span> + 198 <span class="i">$Precision</span> = <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="sc">;</span> + 199 <span class="k">for</span> <span class="i">$RegionID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="w">RegionIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 200 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span> + 201 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span> + 202 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> + 203 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} && <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$FileIndex</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>}<span class="s">)</span> <span class="s">{</span> + 204 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> + 205 <span class="s">}</span> + 206 <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}}<span class="s">)</span> <span class="s">{</span> + 207 <span class="i">$Count</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>}<span class="sc">;</span> + 208 <span class="i">$PercentCount</span> = <span class="s">(</span><span class="i">$Count</span> / <span class="i">$MaxResiduesCount</span><span class="s">)</span> * <span class="n">100</span><span class="sc">;</span> + 209 <span class="i">$PercentCount</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.${Precision}f"</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> + 210 <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">PercentCount</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>} = <span class="i">$PercentCount</span><span class="sc">;</span> + 211 <span class="s">}</span> + 212 <span class="s">}</span> + 213 <span class="s">}</span> + 214 <span class="s">}</span> + 215 + 216 <span class="c"># Generate output files...</span> +<a name="GeneratePercentResidueFrequencyOutFilesForRegions-"></a> 217 <span class="k">sub </span><span class="m">GeneratePercentResidueFrequencyOutFilesForRegions</span> <span class="s">{</span> + 218 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 219 + 220 <span class="c"># Setup rerfernce sequence data...</span> + 221 <span class="k">my</span><span class="s">(</span><span class="i">$RefereceSequenceID</span><span class="cm">,</span> <span class="i">$RefereceSequence</span><span class="s">)</span><span class="sc">;</span> + 222 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 223 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 224 + 225 <span class="k">my</span><span class="s">(</span><span class="i">$RegionID</span><span class="cm">,</span> <span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$ResNum</span><span class="cm">,</span> <span class="i">$Count</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="cm">,</span> <span class="i">$Residue</span><span class="cm">,</span> <span class="i">$RegionNum</span><span class="cm">,</span> <span class="i">$RegionOutFile</span><span class="cm">,</span> <span class="i">$PercentRegionOutFile</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@PercentLineWords</span><span class="s">)</span><span class="sc">;</span> + 226 + 227 <span class="i">$OutFileRoot</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 228 <span class="i">$OutFileExt</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 229 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> + 230 <span class="k">for</span> <span class="i">$RegionID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="w">RegionIDs</span>}}<span class="s">)</span> <span class="s">{</span> + 231 <span class="i">$RegionNum</span>++<span class="sc">;</span> + 232 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span> + 233 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span> + 234 + 235 <span class="i">$RegionOutFile</span> = <span class="q">"${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="sc">;</span> + 236 <span class="i">$PercentRegionOutFile</span> = <span class="q">"${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="sc">;</span> + 237 + 238 <span class="k">print</span> <span class="q">"Generating $RegionOutFile and $PercentRegionOutFile...\n"</span><span class="sc">;</span> + 239 <span class="k">open</span> <span class="w">REGIONOUTFILE</span><span class="cm">,</span> <span class="q">">$RegionOutFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $RegionOutFile: $! \n"</span><span class="sc">;</span> + 240 <span class="k">open</span> <span class="w">PERCENTREGIONOUTFILE</span><span class="cm">,</span> <span class="q">">$PercentRegionOutFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PercentRegionOutFile: $! \n"</span><span class="sc">;</span> + 241 + 242 <span class="c"># Write out reference residue positions as column values....</span> + 243 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 244 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span> + 245 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> + 246 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} && <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$FileIndex</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>}<span class="s">)</span> <span class="s">{</span> + 247 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> + 248 <span class="s">}</span> + 249 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ResNum</span><span class="sc">;</span> + 250 <span class="s">}</span> + 251 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 252 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 253 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 254 + 255 + 256 <span class="c"># Write out row data for each residue; Gap residue is written last...</span> + 257 <span class="j">RESIDUE:</span> <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span> + 258 <span class="k">if</span> <span class="s">(</span><span class="i">$Residue</span> =~ <span class="q">/^Gap$/i</span><span class="s">)</span> <span class="s">{</span> + 259 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span> + 260 <span class="s">}</span> + 261 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 262 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> + 263 <span class="i">@PercentLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 264 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> + 265 + 266 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> + 267 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} && <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$FileIndex</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>}<span class="s">)</span> <span class="s">{</span> + 268 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> + 269 <span class="s">}</span> + 270 <span class="i">$Count</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>}<span class="sc">;</span> + 271 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Count</span><span class="sc">;</span> + 272 <span class="i">$PercentCount</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">PercentCount</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>}<span class="sc">;</span> + 273 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="sc">;</span> + 274 <span class="s">}</span> + 275 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 276 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 277 + 278 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 279 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 280 <span class="s">}</span> + 281 + 282 <span class="c"># Write out data for gap...</span> + 283 <span class="i">$Residue</span> = <span class="q">'Gap'</span><span class="sc">;</span> + 284 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 285 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> + 286 <span class="i">@PercentLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 287 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> + 288 + 289 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> + 290 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} && <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$FileIndex</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>}<span class="s">)</span> <span class="s">{</span> + 291 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> + 292 <span class="s">}</span> + 293 <span class="i">$Count</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>}<span class="sc">;</span> + 294 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Count</span><span class="sc">;</span> + 295 + 296 <span class="i">$PercentCount</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">PercentCount</span>}{<span class="i">$ResNum</span>}{<span class="i">$Residue</span>}<span class="sc">;</span> + 297 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="sc">;</span> + 298 <span class="s">}</span> + 299 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 300 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 301 + 302 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 303 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 304 + 305 <span class="k">close</span> <span class="w">REGIONOUTFILE</span><span class="sc">;</span> + 306 <span class="k">close</span> <span class="w">PERCENTREGIONOUTFILE</span><span class="sc">;</span> + 307 <span class="s">}</span> + 308 <span class="s">}</span> + 309 + 310 <span class="c"># Process option values...</span> +<a name="ProcessOptions-"></a> 311 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> + 312 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 313 + 314 <span class="c"># Setup analysis mode...</span> + 315 <span class="i">$OptionsInfo</span>{<span class="w">CalculatePercentIdentityMatrix</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(PercentIdentityMatrix|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 316 <span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^(ResidueFrequencyAnalysis|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 317 + 318 <span class="c"># Setup delimiter and quotes...</span> + 319 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span> + 320 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/yes/i</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 321 + 322 <span class="c"># Setup reference sequence and regions for residue frequence analysis...</span> + 323 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRefereceSequence</span>} = <span class="i">$Options</span>{<span class="w">referencesequence</span>}<span class="sc">;</span> + 324 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegion</span>} = <span class="i">$Options</span>{<span class="w">region</span>}<span class="sc">;</span> + 325 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 326 + 327 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedRegions</span><span class="s">)</span><span class="sc">;</span> + 328 <span class="i">@SpecifiedRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 329 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">region</span>} =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span> + 330 <span class="i">@SpecifiedRegions</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegion</span>}<span class="sc">;</span> + 331 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedRegions</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 332 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"</span><span class="sc">;</span> + 333 <span class="s">}</span> + 334 <span class="c"># Make sure EndResNum > StartResNum...</span> + 335 <span class="k">my</span><span class="s">(</span><span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$RegionNum</span><span class="s">)</span><span class="sc">;</span> + 336 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> + 337 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> <= <span class="i">$#SpecifiedRegions</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 338 <span class="i">$StartResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 339 <span class="i">$EndResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> + 340 <span class="i">$RegionNum</span>++<span class="sc">;</span> + 341 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$StartResNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 342 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be a positive integer for region $RegionNum.\n"</span><span class="sc">;</span> + 343 <span class="s">}</span> + 344 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$EndResNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 345 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $EndResNum, must be a positive integer for region $RegionNum.\n"</span><span class="sc">;</span> + 346 <span class="s">}</span> + 347 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> >= <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> + 348 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be smaller than end residue number, $EndResNum, for region $RegionNum.\n"</span><span class="sc">;</span> + 349 <span class="s">}</span> + 350 <span class="s">}</span> + 351 <span class="s">}</span> + 352 <span class="k">else</span> <span class="s">{</span> + 353 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">region</span>} !~ <span class="q">/^UseCompleteSequence$/i</span><span class="s">)</span> <span class="s">{</span> + 354 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"</span><span class="sc">;</span> + 355 <span class="s">}</span> + 356 <span class="s">}</span> + 357 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}}<span class="cm">,</span> <span class="i">@SpecifiedRegions</span><span class="sc">;</span> + 358 + 359 <span class="c"># Miscellaneous options...</span> + 360 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> + 361 <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> + 362 <span class="i">$OptionsInfo</span>{<span class="w">RegionResiduesMode</span>} = <span class="i">$Options</span>{<span class="w">regionresiduesmode</span>}<span class="sc">;</span> + 363 + 364 <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> + 365 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 366 <span class="s">}</span> + 367 + 368 <span class="c"># Retrieve information about sequence files...</span> +<a name="RetrieveSequenceFilesInfo-"></a> 369 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span> + 370 <span class="k">my</span><span class="s">(</span><span class="i">$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">$RefereceSequence</span><span class="cm">,</span> <span class="i">$RefereceSequenceID</span><span class="cm">,</span> <span class="i">$RefereceSequenceLen</span><span class="cm">,</span> <span class="i">$RefereceSequenceWithNoGaps</span><span class="cm">,</span> <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="cm">,</span> <span class="i">$RefereceSequenceRegionCount</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">$OutFileExt</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$SpecifiedRefereceSequence</span><span class="cm">,</span> <span class="i">@SpecifiedRegions</span><span class="cm">,</span> <span class="i">@RefereceSequenceRegions</span><span class="s">)</span><span class="sc">;</span> + 371 + 372 <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 373 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 374 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 375 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 376 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 377 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 378 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 379 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 380 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 381 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 382 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 383 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 384 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 385 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 386 + 387 <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> + 388 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 389 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 390 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 391 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 392 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="q">'NotSupported'</span><span class="sc">;</span> + 393 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 394 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 395 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 396 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 397 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 398 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 399 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 400 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 401 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 402 + 403 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span><span class="s">)</span> <span class="s">{</span> + 404 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n"</span><span class="sc">;</span> + 405 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 406 <span class="s">}</span> + 407 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> + 408 + 409 <span class="s">(</span><span class="i">$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> + 410 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span> + 411 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n"</span><span class="sc">;</span> + 412 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 413 <span class="s">}</span> + 414 + 415 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> + 416 + 417 <span class="i">$SequenceCount</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span> + 418 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceCount</span><span class="s">)</span> <span class="s">{</span> + 419 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence data is missing.\n"</span><span class="sc">;</span> + 420 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 421 <span class="s">}</span> + 422 + 423 <span class="c"># Make sure all sequence lengths are identical...</span> + 424 <span class="k">if</span> <span class="s">(</span>!<span class="i">AreSequenceLengthsIdentical</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 425 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence legths are not identical.\n"</span><span class="sc">;</span> + 426 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 427 <span class="s">}</span> + 428 <span class="i">$SpecifiedRefereceSequence</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRefereceSequence</span>}<span class="sc">;</span> + 429 <span class="c"># Make sure reference sequence ID is valid...</span> + 430 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRefereceSequence</span> =~ <span class="q">/^UseFirstSequenceID$/i</span><span class="s">)</span> <span class="s">{</span> + 431 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span> + 432 <span class="s">}</span> + 433 <span class="k">else</span> <span class="s">{</span> + 434 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$SpecifiedRefereceSequence</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 435 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Rreference sequence ID, $SpecifiedRefereceSequence, specified using option \"--referencesequence\" is missing.\n"</span><span class="sc">;</span> + 436 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 437 <span class="s">}</span> + 438 <span class="i">$RefereceSequenceID</span> = <span class="i">$SpecifiedRefereceSequence</span><span class="sc">;</span> + 439 <span class="s">}</span> + 440 + 441 <span class="c"># Make sure sequence regions corresponding to reference sequence are valid...</span> + 442 <span class="i">@RefereceSequenceRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 443 <span class="i">$RefereceSequenceRegionCount</span> = <span class="n">0</span><span class="sc">;</span> + 444 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$RefereceSequenceID</span>}<span class="sc">;</span> + 445 <span class="i">$RefereceSequenceLen</span> = <span class="k">length</span> <span class="i">$RefereceSequence</span><span class="sc">;</span> + 446 + 447 <span class="i">$RefereceSequenceWithNoGaps</span> = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$RefereceSequence</span><span class="s">)</span><span class="sc">;</span> + 448 <span class="i">$RefereceSequenceWithNoGapsLen</span> = <span class="k">length</span> <span class="i">$RefereceSequenceWithNoGaps</span><span class="sc">;</span> + 449 + 450 <span class="i">@SpecifiedRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 451 <span class="k">push</span> <span class="i">@SpecifiedRegions</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}}<span class="sc">;</span> + 452 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedRegions</span><span class="s">)</span> <span class="s">{</span> + 453 <span class="c"># Make sure specified regions are valid...</span> + 454 <span class="k">my</span><span class="s">(</span><span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$RegionIndex</span><span class="cm">,</span> <span class="i">$RegionNum</span><span class="s">)</span><span class="sc">;</span> + 455 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> + 456 <span class="k">for</span> <span class="s">(</span><span class="i">$RegionIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$RegionIndex</span> <= <span class="i">$#SpecifiedRegions</span><span class="sc">;</span> <span class="i">$RegionIndex</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 457 <span class="i">$StartResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$RegionIndex</span>]<span class="sc">;</span> + 458 <span class="i">$EndResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$RegionIndex</span> + <span class="n">1</span>]<span class="sc">;</span> + 459 <span class="i">$RegionNum</span>++<span class="sc">;</span> + 460 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span> + 461 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> > <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span> <span class="s">{</span> + 462 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be smaller the sequence length, $RefereceSequenceWithNoGapsLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"</span><span class="sc">;</span> + 463 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 464 <span class="s">}</span> + 465 <span class="k">if</span> <span class="s">(</span><span class="i">$EndResNum</span> > <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span> <span class="s">{</span> + 466 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The end residue number, $EndResNum, must be smaller the sequence length, $RefereceSequenceWithNoGapsLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"</span><span class="sc">;</span> + 467 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 468 <span class="s">}</span> + 469 <span class="s">}</span> + 470 <span class="k">else</span> <span class="s">{</span> + 471 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> > <span class="i">$RefereceSequenceLen</span><span class="s">)</span> <span class="s">{</span> + 472 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The start residue number, $StartResNum, must be smaller the sequence length, $RefereceSequenceLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum.\n"</span><span class="sc">;</span> + 473 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 474 <span class="s">}</span> + 475 <span class="k">if</span> <span class="s">(</span><span class="i">$EndResNum</span> > <span class="i">$RefereceSequenceLen</span><span class="s">)</span> <span class="s">{</span> + 476 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The value specified, $Options{region}, for option \"--region\" is not valid: The end residue number, $EndResNum, must be smaller the sequence length, $RefereceSequenceLen, of reference sequence ID, $RefereceSequenceID, in region $RegionNum.\n"</span><span class="sc">;</span> + 477 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 478 <span class="s">}</span> + 479 <span class="s">}</span> + 480 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="s">(</span><span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span><span class="sc">;</span> + 481 <span class="s">}</span> + 482 <span class="i">$RefereceSequenceRegionCount</span> = <span class="i">$RegionNum</span><span class="sc">;</span> + 483 <span class="s">}</span> + 484 <span class="k">else</span> <span class="s">{</span> + 485 <span class="c"># Use complete sequence corresponding to reference sequence ID...</span> + 486 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span> + 487 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span><span class="sc">;</span> + 488 <span class="s">}</span> + 489 <span class="k">else</span> <span class="s">{</span> + 490 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="i">$RefereceSequenceLen</span><span class="s">)</span><span class="sc">;</span> + 491 <span class="s">}</span> + 492 <span class="i">$RefereceSequenceRegionCount</span> = <span class="n">1</span><span class="sc">;</span> + 493 <span class="s">}</span> + 494 <span class="c"># Setup output file names...</span> + 495 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> + 496 <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> + 497 <span class="i">$FileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> + 498 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span> + 499 <span class="i">$FileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> + 500 <span class="s">}</span> + 501 <span class="i">$OutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span> + 502 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SequenceFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 503 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> + 504 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> + 505 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> + 506 <span class="s">}</span> + 507 <span class="k">else</span> <span class="s">{</span> + 508 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> + 509 <span class="s">}</span> + 510 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> + 511 <span class="s">}</span> + 512 <span class="k">else</span> <span class="s">{</span> + 513 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> + 514 <span class="s">}</span> + 515 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> + 516 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculatePercentIdentityMatrix</span>}<span class="s">)</span> <span class="s">{</span> + 517 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}PercentIdentityMatrix.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> + 518 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}PercentIdentityMatrix.${OutFileExt} already exists\n"</span><span class="sc">;</span> + 519 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 520 <span class="s">}</span> + 521 <span class="s">}</span> + 522 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span> + 523 <span class="k">my</span><span class="s">(</span><span class="i">$RegionNum</span><span class="s">)</span><span class="sc">;</span> + 524 <span class="k">for</span> <span class="i">$RegionNum</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$RefereceSequenceRegionCount</span><span class="s">)</span> <span class="s">{</span> + 525 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> + 526 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"</span><span class="sc">;</span> + 527 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 528 <span class="s">}</span> + 529 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> + 530 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"</span><span class="sc">;</span> + 531 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 532 <span class="s">}</span> + 533 <span class="s">}</span> + 534 <span class="s">}</span> + 535 <span class="s">}</span> + 536 + 537 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> + 538 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> + 539 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span> + 540 + 541 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span> + 542 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="i">$SequenceCount</span><span class="sc">;</span> + 543 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceID</span><span class="sc">;</span> + 544 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequence</span><span class="sc">;</span> + 545 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceLen</span><span class="sc">;</span> + 546 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceWithNoGaps</span><span class="sc">;</span> + 547 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="sc">;</span> + 548 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@RefereceSequenceRegions</span><span class="sc">;</span> + 549 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceRegionCount</span><span class="sc">;</span> + 550 + 551 <span class="c"># Setup residue codes...</span> + 552 <span class="i">SetupSequenceFileResidueCodes</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span> + 553 <span class="s">}</span> + 554 <span class="s">}</span> + 555 +<a name="SetupSequenceFileResidueCodes-"></a> 556 <span class="k">sub </span><span class="m">SetupSequenceFileResidueCodes</span> <span class="s">{</span> + 557 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 558 <span class="k">my</span><span class="s">(</span><span class="i">$Residue</span><span class="cm">,</span> <span class="i">@ResidueCodesList</span><span class="cm">,</span> <span class="i">%ResidueCodesMap</span><span class="s">)</span><span class="sc">;</span> + 559 + 560 <span class="c"># Initialize</span> + 561 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}[<span class="i">$FileIndex</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 562 + 563 <span class="i">%ResidueCodesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 564 <span class="i">@ResidueCodesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 565 + 566 <span class="c"># Setup standard amino acids and nucleic acids one letter codes...</span> + 567 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RegionResiduesMode</span>} =~ <span class="q">/^AminoAcids$/i</span><span class="s">)</span> <span class="s">{</span> + 568 <span class="i">@ResidueCodesList</span> = <span class="i">AminoAcids::GetAminoAcids</span><span class="s">(</span><span class="q">'OneLetterCode'</span><span class="s">)</span><span class="sc">;</span> + 569 <span class="s">}</span> + 570 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RegionResiduesMode</span>} =~ <span class="q">/^NucleicAcids$/i</span><span class="s">)</span> <span class="s">{</span> + 571 <span class="k">push</span> <span class="i">@ResidueCodesList</span><span class="cm">,</span> <span class="s">(</span><span class="q">'A'</span><span class="cm">,</span> <span class="q">'G'</span><span class="cm">,</span> <span class="q">'T'</span><span class="cm">,</span> <span class="q">'U'</span><span class="cm">,</span> <span class="q">'C'</span><span class="s">)</span><span class="sc">;</span> + 572 <span class="s">}</span> + 573 <span class="k">push</span> <span class="i">@ResidueCodesList</span><span class="cm">,</span> <span class="q">'Gap'</span><span class="sc">;</span> + 574 <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="i">@ResidueCodesList</span><span class="s">)</span> <span class="s">{</span> + 575 <span class="i">$ResidueCodesMap</span>{<span class="i">$Residue</span>} = <span class="i">$Residue</span><span class="sc">;</span> + 576 <span class="s">}</span> + 577 + 578 <span class="c"># Go over all the residues in all the sequences and add missing ones to the list...</span> + 579 <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="cm">,</span> <span class="i">$ResIndex</span><span class="s">)</span><span class="sc">;</span> + 580 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> + 581 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> + 582 <span class="j">RES:</span> <span class="k">for</span> <span class="i">$ResIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 583 <span class="i">$Residue</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$ResIndex</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 584 <span class="k">if</span> <span class="s">(</span><span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 585 <span class="k">next</span> <span class="j">RES</span><span class="sc">;</span> + 586 <span class="s">}</span> + 587 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ResidueCodesMap</span>{<span class="i">$Residue</span>}<span class="s">)</span> <span class="s">{</span> + 588 <span class="k">next</span> <span class="j">RES</span><span class="sc">;</span> + 589 <span class="s">}</span> + 590 <span class="k">push</span> <span class="i">@ResidueCodesList</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> + 591 <span class="i">$ResidueCodesMap</span>{<span class="i">$Residue</span>} = <span class="i">$Residue</span><span class="sc">;</span> + 592 <span class="s">}</span> + 593 <span class="s">}</span> + 594 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}[<span class="i">$FileIndex</span>]}<span class="cm">,</span> <span class="i">@ResidueCodesList</span><span class="sc">;</span> + 595 <span class="s">}</span> + 596 + 597 <span class="c"># Setup regions data for performing residue frequency analysis...</span> +<a name="SetupSequenceRegionsData-"></a> 598 <span class="k">sub </span><span class="m">SetupSequenceRegionsData</span> <span class="s">{</span> + 599 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RefereceSequence</span><span class="cm">,</span> <span class="i">$RefereceSequenceLen</span><span class="cm">,</span> <span class="i">$RegionID</span><span class="cm">,</span> <span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="cm">,</span> <span class="i">$RegionIndex</span><span class="cm">,</span> <span class="i">$RegionNum</span><span class="cm">,</span> <span class="i">$NoGapResNum</span><span class="cm">,</span> <span class="i">$ResNum</span><span class="cm">,</span> <span class="i">$ResIndex</span><span class="cm">,</span> <span class="i">$Residue</span><span class="cm">,</span> <span class="i">$ResidueCode</span><span class="cm">,</span> <span class="i">@RefereceSequenceRegions</span><span class="s">)</span><span class="sc">;</span> + 600 + 601 + 602 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 603 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 604 + 605 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span> + 606 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">IsGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 607 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">NoGapToGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 608 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">GapToNoGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 609 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 610 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]{<span class="w">RegionIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 611 + 612 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> + 613 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 614 <span class="s">}</span> + 615 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span> + 616 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 617 <span class="s">}</span> + 618 + 619 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 620 <span class="i">$RefereceSequenceLen</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 621 + 622 <span class="c"># Setup residue number mapping and gap status for refernece sequence...</span> + 623 <span class="i">$NoGapResNum</span> = <span class="n">0</span><span class="sc">;</span> + 624 <span class="i">$ResNum</span> = <span class="n">0</span><span class="sc">;</span> + 625 <span class="k">for</span> <span class="i">$ResIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$RefereceSequenceLen</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 626 <span class="i">$ResNum</span>++<span class="sc">;</span> + 627 <span class="i">$Residue</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$RefereceSequence</span><span class="cm">,</span> <span class="i">$ResIndex</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 628 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>} = <span class="n">1</span><span class="sc">;</span> + 629 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 630 <span class="i">$NoGapResNum</span>++<span class="sc">;</span> + 631 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>} = <span class="n">0</span><span class="sc">;</span> + 632 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">NoGapToGap</span>}{<span class="i">$NoGapResNum</span>} = <span class="i">$ResNum</span><span class="sc">;</span> + 633 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">GapToNoGap</span>}{<span class="i">$ResNum</span>} = <span class="i">$NoGapResNum</span><span class="sc">;</span> + 634 <span class="s">}</span> + 635 <span class="s">}</span> + 636 <span class="c"># Map residue numbers for specified regions to the reference residue in input sequence/alignment files</span> + 637 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> + 638 <span class="i">@RefereceSequenceRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 639 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}[<span class="i">$Index</span>]}<span class="sc">;</span> + 640 <span class="k">for</span> <span class="s">(</span><span class="i">$RegionIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$RegionIndex</span> <= <span class="i">$#RefereceSequenceRegions</span><span class="sc">;</span> <span class="i">$RegionIndex</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 641 <span class="i">$StartResNum</span> = <span class="i">$RefereceSequenceRegions</span>[<span class="i">$RegionIndex</span>]<span class="sc">;</span> + 642 <span class="i">$EndResNum</span> = <span class="i">$RefereceSequenceRegions</span>[<span class="i">$RegionIndex</span> + <span class="n">1</span>]<span class="sc">;</span> + 643 <span class="i">$RegionNum</span>++<span class="sc">;</span> + 644 <span class="i">$RegionID</span> = <span class="q">"Region${RegionNum}"</span><span class="sc">;</span> + 645 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span> + 646 <span class="c"># Map residue numbers to the reference sequence residue numbers to account for any ignored gaps...</span> + 647 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">NoGapToGap</span>}{<span class="i">$StartResNum</span>}<span class="sc">;</span> + 648 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">NoGapToGap</span>}{<span class="i">$EndResNum</span>}<span class="sc">;</span> + 649 <span class="s">}</span> + 650 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]{<span class="w">RegionIDs</span>}}<span class="cm">,</span> <span class="i">$RegionID</span><span class="sc">;</span> + 651 <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>} = <span class="i">$StartResNum</span><span class="sc">;</span> + 652 <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>} = <span class="i">$EndResNum</span><span class="sc">;</span> + 653 + 654 <span class="c"># Initialize data for residue codes...</span> + 655 <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> + 656 <span class="k">for</span> <span class="i">$ResidueCode</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span> + 657 <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]{<span class="i">$RegionID</span>}{<span class="w">Count</span>}{<span class="i">$ResNum</span>}{<span class="i">$ResidueCode</span>} = <span class="n">0</span><span class="sc">;</span> + 658 <span class="s">}</span> + 659 <span class="s">}</span> + 660 <span class="s">}</span> + 661 <span class="s">}</span> + 662 <span class="s">}</span> + 663 + 664 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> +<a name="SetupScriptUsage-"></a> 665 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> + 666 + 667 <span class="c"># Retrieve all the options...</span> + 668 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 669 <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">'yes'</span><span class="sc">;</span> + 670 <span class="i">$Options</span>{<span class="w">regionresiduesmode</span>} = <span class="q">'None'</span><span class="sc">;</span> + 671 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'PercentIdentityMatrix'</span><span class="sc">;</span> + 672 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> + 673 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span> + 674 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span> + 675 <span class="i">$Options</span>{<span class="w">referencesequence</span>} = <span class="q">'UseFirstSequenceID'</span><span class="sc">;</span> + 676 <span class="i">$Options</span>{<span class="w">region</span>} = <span class="q">'UseCompleteSequence'</span><span class="sc">;</span> + 677 + 678 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"ignoregaps|i=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"precision|p=i"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"referencesequence=s"</span><span class="cm">,</span> <span class="q">"region=s"</span><span class="cm">,</span> <span class="q">"regionresiduesmode=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 679 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> + 680 <span class="s">}</span> + 681 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> + 682 <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> + 683 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> + 684 <span class="s">}</span> + 685 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> + 686 <span class="s">}</span> + 687 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> + 688 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ignoregaps}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> + 689 <span class="s">}</span> + 690 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">regionresiduesmode</span>} !~ <span class="q">/^(AminoAcids|NucleicAcids|None)$/i</span><span class="s">)</span> <span class="s">{</span> + 691 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{regionresiduesmode}, for option \"--regionresiduesmode\" is not valid. Allowed values: AminoAcids, NucleicAcids or None\n"</span><span class="sc">;</span> + 692 <span class="s">}</span> + 693 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(PercentIdentityMatrix|ResidueFrequencyAnalysis|All)$/i</span><span class="s">)</span> <span class="s">{</span> + 694 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: PercentIdentityMatrix, ResidueFrequencyAnalysis or All\n"</span><span class="sc">;</span> + 695 <span class="s">}</span> + 696 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> + 697 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> + 698 <span class="s">}</span> + 699 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> + 700 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> + 701 <span class="s">}</span> + 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 703 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> + 704 <span class="s">}</span> + 705 <span class="s">}</span> + 706 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>