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author	deepakjadmin
date	Wed, 20 Jan 2016 09:23:18 -0500
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0 4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	1 <html>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	2 <head>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	3 <title>MayaChemTools:Code:AnalyzeSequenceFilesData.pl</title>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	6 </head>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	8 <br/>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	9 <center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	11 </center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	12 <br/>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	13 <pre>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	14 1 #!/usr/bin/perl -w
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	15 2 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	16 3 <span class="c"># $RCSfile: AnalyzeSequenceFilesData.pl,v $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	17 4 <span class="c"># $Date: 2015/02/28 20:46:04 $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	18 5 <span class="c"># $Revision: 1.33 $</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	19 6 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	21 8 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	23 10 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	24 11 <span class="c"># This file is part of MayaChemTools.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	25 12 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	29 16 <span class="c"># later version.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	30 17 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	34 21 <span class="c"># details.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	35 22 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	40 27 <span class="c">#</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	41 28
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	43 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	50 37 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	51 38 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	52 39 <span class="k">use</span> <span class="w">NucleicAcids</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	53 40
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	54 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	55 42
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	56 43 <span class="c"># Autoflush STDOUT</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	57 44 <span class="i">$\|</span> = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	58 45
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	59 46 <span class="c"># Starting message...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	60 47 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	61 48 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	62 49 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	63 50
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	64 51 <span class="c"># Setup script usage message...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	65 52 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	66 53 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	67 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	68 55 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	69 56
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	70 57 <span class="c"># Expand wild card file names...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	71 58 <span class="k">my</span><span class="s">(</span><span class="i">@SequenceFilesList</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	72 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	73 60
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	74 61 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	75 62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	76 63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	77 64
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	78 65 <span class="c"># Set up information about input files...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	79 66 <span class="k">print</span> <span class="q">"Checking input sequence file(s)...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	80 67 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	81 68 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	82 69 <span class="i">SetupSequenceRegionsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	83 70
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	84 71 <span class="c"># Process input files..</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	85 72 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	86 73 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	87 74 <span class="k">print</span> <span class="q">"\nProcessing sequence files...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	88 75 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	89 76 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	90 77 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	91 78 <span class="k">print</span> <span class="q">"\nProcessing file $SequenceFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	92 79 <span class="i">AnalyzeSequenceFileData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	93 80 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	94 81 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	95 82 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	96 83
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	97 84 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	98 85 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	99 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	100 87
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	101 88 <span class="c">###############################################################################</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	102 89
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	103 90 <span class="c"># Analyze sequence file...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	104 <a name="AnalyzeSequenceFileData-"></a> 91 <span class="k">sub </span><span class="m">AnalyzeSequenceFileData</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	105 92 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	106 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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	107 94
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	108 95 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	109 96
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	110 97 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $SequenceFile: $! \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	111 98 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	112 99 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	113 100
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	114 101 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculatePercentIdentityMatrix</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	115 102 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	116 103 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	117 104 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	118 105 <span class="i">PerformResidueFrequencyAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	119 106 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	120 107 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	121 108
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	122 109 <span class="c"># Calculate percent identity matrix...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	123 <a name="CalculatePercentIdentityMatrix-"></a> 110 <span class="k">sub </span><span class="m">CalculatePercentIdentityMatrix</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	124 111 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	125 112 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	126 113
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	127 114 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	128 115 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	129 116
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	130 117 <span class="k">print</span> <span class="q">"Generating percent identity matrix file $PercentIdentityMatrixFile...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	131 118 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PercentIdentityMatrixFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Can't open $PercentIdentityMatrixFile: $!\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	132 119
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	133 120 <span class="c"># Write out column labels...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	134 121 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	135 122 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	136 123 <span class="k">for</span> <span class="i">$ColID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	137 124 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ColID</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	138 125 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	139 126 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	140 127 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	141 128
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	142 129 <span class="c"># Write out rows...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	143 130 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	144 131 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	145 132 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$RowID</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	146 133 <span class="k">for</span> <span class="i">$ColID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	147 134 <span class="i">$PercentIdentity</span> = <span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">PercentIdentity</span>}{<span class="i">$RowID</span>}{<span class="i">$ColID</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	148 135 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PercentIdentity</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	149 136 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	150 137 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	151 138 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	152 139 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	153 140 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	154 141 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	155 142
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	156 143 <span class="c"># Perform frequency analysis...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	157 <a name="PerformResidueFrequencyAnalysis-"></a> 144 <span class="k">sub </span><span class="m">PerformResidueFrequencyAnalysis</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	158 145 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	159 146
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	160 147 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	161 148 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	162 149 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	163 150 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	164 151
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	165 152 <span class="c"># Count residues...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	166 <a name="CountResiduesInRegions-"></a> 153 <span class="k">sub </span><span class="m">CountResiduesInRegions</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	167 154 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	168 155
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	169 156 <span class="c"># Setup rerfernce sequence data...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	170 157 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	171 158 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	172 159 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	173 160
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	174 161 <span class="c"># Count residues...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	175 162 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	176 163 <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">$FileIndex</span>]{<span class="w">RegionIDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	177 164 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	178 165 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	179 166 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	180 167 <span class="i">$ResIndex</span> = <span class="i">$ResNum</span> - <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	181 168 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	182 169 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	183 170 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	184 171 <span class="c"># Go over residues in column $ResNum in all the sequences...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	185 172 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	186 173 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	187 174 <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">$ResIndex</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	188 175 <span class="k">if</span> <span class="s">(</span><span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	189 176 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	190 177 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	191 178 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	192 179 <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">$Residue</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	193 180 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	194 181 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	195 182 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	196 183 <span class="c"># Internal error...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	197 184 <span class="k">print</span> <span class="q">"Warning: Ignoring residue $Residue in sequence $ID during ResidueFrequencyAnalysis calculation: Unknown residue...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	198 185 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	199 186 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	200 187 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	201 188 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	202 189 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	203 190 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	204 191
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	205 192 <span class="c"># Calculate percent frequency for various residues in the sequence regions...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	206 <a name="CalculatePercentResidueFrequencyInRegions-"></a> 193 <span class="k">sub </span><span class="m">CalculatePercentResidueFrequencyInRegions</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	207 194 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	208 195 <span class="k">my</span><span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	209 196
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	210 197 <span class="i">$MaxResiduesCount</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	211 198 <span class="i">$Precision</span> = <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	212 199 <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">$FileIndex</span>]{<span class="w">RegionIDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	213 200 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	214 201 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	215 202 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	216 203 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	217 204 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	218 205 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	219 206 <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">$ResNum</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	220 207 <span class="i">$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">$Residue</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	221 208 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	222 209 <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">$PercentCount</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	223 210 <span class="i">$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">$PercentCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	224 211 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	225 212 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	226 213 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	227 214 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	228 215
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	229 216 <span class="c"># Generate output files...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	230 <a name="GeneratePercentResidueFrequencyOutFilesForRegions-"></a> 217 <span class="k">sub </span><span class="m">GeneratePercentResidueFrequencyOutFilesForRegions</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	231 218 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	232 219
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	233 220 <span class="c"># Setup rerfernce sequence data...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	234 221 <span class="k">my</span><span class="s">(</span><span class="i">$RefereceSequenceID</span><span class="cm">,</span> <span class="i">$RefereceSequence</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	235 222 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	236 223 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	237 224
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	238 225 <span class="k">my</span><span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	239 226
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	240 227 <span class="i">$OutFileRoot</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	241 228 <span class="i">$OutFileExt</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	242 229 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	243 230 <span class="k">for</span> <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	244 231 <span class="i">$RegionNum</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	245 232 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	246 233 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	247 234
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	248 235 <span class="i">$RegionOutFile</span> = <span class="q">"${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	249 236 <span class="i">$PercentRegionOutFile</span> = <span class="q">"${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	250 237
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	251 238 <span class="k">print</span> <span class="q">"Generating $RegionOutFile and $PercentRegionOutFile...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	252 239 <span class="k">open</span> <span class="w">REGIONOUTFILE</span><span class="cm">,</span> <span class="q">">$RegionOutFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $RegionOutFile: $! \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	253 240 <span class="k">open</span> <span class="w">PERCENTREGIONOUTFILE</span><span class="cm">,</span> <span class="q">">$PercentRegionOutFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PercentRegionOutFile: $! \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	254 241
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	255 242 <span class="c"># Write out reference residue positions as column values....</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	256 243 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	257 244 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	258 245 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	259 246 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	260 247 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	261 248 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	262 249 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ResNum</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	263 250 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	264 251 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	265 252 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	266 253 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	267 254
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	268 255
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	269 256 <span class="c"># Write out row data for each residue; Gap residue is written last...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	270 257 <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">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	271 258 <span class="k">if</span> <span class="s">(</span><span class="i">$Residue</span> =~ <span class="q">/^Gap$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	272 259 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	273 260 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	274 261 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	275 262 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	276 263 <span class="i">@PercentLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	277 264 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	278 265
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	279 266 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	280 267 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	281 268 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	282 269 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	283 270 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	284 271 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Count</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	285 272 <span class="i">$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">$Residue</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	286 273 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	287 274 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	288 275 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	289 276 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	290 277
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	291 278 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	292 279 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	293 280 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	294 281
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	295 282 <span class="c"># Write out data for gap...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	296 283 <span class="i">$Residue</span> = <span class="q">'Gap'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	297 284 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	298 285 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	299 286 <span class="i">@PercentLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	300 287 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	301 288
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	302 289 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	303 290 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	304 291 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	305 292 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	306 293 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	307 294 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Count</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	308 295
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	309 296 <span class="i">$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">$Residue</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	310 297 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	311 298 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	312 299 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	313 300 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	314 301
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	315 302 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	316 303 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	317 304
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	318 305 <span class="k">close</span> <span class="w">REGIONOUTFILE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	319 306 <span class="k">close</span> <span class="w">PERCENTREGIONOUTFILE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	320 307 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	321 308 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	322 309
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	323 310 <span class="c"># Process option values...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	324 <a name="ProcessOptions-"></a> 311 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	325 312 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	326 313
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	327 314 <span class="c"># Setup analysis mode...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	328 315 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	329 316 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	330 317
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	331 318 <span class="c"># Setup delimiter and quotes...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	332 319 <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">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	333 320 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/yes/i</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	334 321
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	335 322 <span class="c"># Setup reference sequence and regions for residue frequence analysis...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	336 323 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRefereceSequence</span>} = <span class="i">$Options</span>{<span class="w">referencesequence</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	337 324 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegion</span>} = <span class="i">$Options</span>{<span class="w">region</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	338 325 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	339 326
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	340 327 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedRegions</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	341 328 <span class="i">@SpecifiedRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	342 329 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">region</span>} =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	343 330 <span class="i">@SpecifiedRegions</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegion</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	344 331 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	345 332 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	346 333 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	347 334 <span class="c"># Make sure EndResNum > StartResNum...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	348 335 <span class="k">my</span><span class="s">(</span><span class="i">$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">$RegionNum</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	349 336 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	350 337 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	351 338 <span class="i">$StartResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	352 339 <span class="i">$EndResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	353 340 <span class="i">$RegionNum</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	354 341 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$StartResNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	355 342 <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 $RegionNum.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	356 343 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	357 344 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$EndResNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	358 345 <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 $RegionNum.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	359 346 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	360 347 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> >= <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	361 348 <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 $RegionNum.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	362 349 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	363 350 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	364 351 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	365 352 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">region</span>} !~ <span class="q">/^UseCompleteSequence$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	367 354 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	368 355 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	369 356 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	370 357 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}}<span class="cm">,</span> <span class="i">@SpecifiedRegions</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	371 358
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	372 359 <span class="c"># Miscellaneous options...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	373 360 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	374 361 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	375 362 <span class="i">$OptionsInfo</span>{<span class="w">RegionResiduesMode</span>} = <span class="i">$Options</span>{<span class="w">regionresiduesmode</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	376 363
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	377 364 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	378 365 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	379 366 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	380 367
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	381 368 <span class="c"># Retrieve information about sequence files...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	382 <a name="RetrieveSequenceFilesInfo-"></a> 369 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	383 370 <span class="k">my</span><span class="s">(</span><span class="i">$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">$SpecifiedRefereceSequence</span><span class="cm">,</span> <span class="i">@SpecifiedRegions</span><span class="cm">,</span> <span class="i">@RefereceSequenceRegions</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	384 371
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	385 372 <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	386 373 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	387 374 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	388 375 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	389 376 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	390 377 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	391 378 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	392 379 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	393 380 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	394 381 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	395 382 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	396 383 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	397 384 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	398 385 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	399 386
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	400 387 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	401 388 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	402 389 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	403 390 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	404 391 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	405 392 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="q">'NotSupported'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	406 393 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	407 394 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	408 395 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	409 396 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	410 397 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	411 398 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	412 399 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	413 400 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	414 401 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	415 402
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	416 403 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	417 404 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	418 405 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	419 406 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	420 407 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	421 408
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	422 409 <span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	423 410 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	424 411 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	425 412 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	426 413 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	427 414
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	428 415 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	429 416
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	430 417 <span class="i">$SequenceCount</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	431 418 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceCount</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	432 419 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence data is missing.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	433 420 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	434 421 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	435 422
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	436 423 <span class="c"># Make sure all sequence lengths are identical...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	437 424 <span class="k">if</span> <span class="s">(</span>!<span class="i">AreSequenceLengthsIdentical</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	438 425 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence legths are not identical.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	439 426 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	440 427 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	441 428 <span class="i">$SpecifiedRefereceSequence</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRefereceSequence</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	442 429 <span class="c"># Make sure reference sequence ID is valid...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	443 430 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRefereceSequence</span> =~ <span class="q">/^UseFirstSequenceID$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	444 431 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	445 432 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	446 433 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	447 434 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$SpecifiedRefereceSequence</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	448 435 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Rreference sequence ID, $SpecifiedRefereceSequence, specified using option \"--referencesequence\" is missing.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	449 436 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	450 437 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	451 438 <span class="i">$RefereceSequenceID</span> = <span class="i">$SpecifiedRefereceSequence</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	452 439 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	453 440
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	454 441 <span class="c"># Make sure sequence regions corresponding to reference sequence are valid...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	455 442 <span class="i">@RefereceSequenceRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	456 443 <span class="i">$RefereceSequenceRegionCount</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	457 444 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$RefereceSequenceID</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	458 445 <span class="i">$RefereceSequenceLen</span> = <span class="k">length</span> <span class="i">$RefereceSequence</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	459 446
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	460 447 <span class="i">$RefereceSequenceWithNoGaps</span> = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$RefereceSequence</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	461 448 <span class="i">$RefereceSequenceWithNoGapsLen</span> = <span class="k">length</span> <span class="i">$RefereceSequenceWithNoGaps</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	462 449
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	463 450 <span class="i">@SpecifiedRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	464 451 <span class="k">push</span> <span class="i">@SpecifiedRegions</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	465 452 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedRegions</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	466 453 <span class="c"># Make sure specified regions are valid...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	467 454 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	468 455 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	469 456 <span class="k">for</span> <span class="s">(</span><span class="i">$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">$RegionIndex</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	470 457 <span class="i">$StartResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$RegionIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	471 458 <span class="i">$EndResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$RegionIndex</span> + <span class="n">1</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	472 459 <span class="i">$RegionNum</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	473 460 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	474 461 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> > <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	475 462 <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 $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	476 463 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	477 464 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	478 465 <span class="k">if</span> <span class="s">(</span><span class="i">$EndResNum</span> > <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	479 466 <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 $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	480 467 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	481 468 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	482 469 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	483 470 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	484 471 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> > <span class="i">$RefereceSequenceLen</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	485 472 <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 $RegionNum.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	486 473 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	487 474 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	488 475 <span class="k">if</span> <span class="s">(</span><span class="i">$EndResNum</span> > <span class="i">$RefereceSequenceLen</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	489 476 <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 $RegionNum.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	490 477 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	491 478 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	492 479 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	493 480 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="s">(</span><span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	494 481 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	495 482 <span class="i">$RefereceSequenceRegionCount</span> = <span class="i">$RegionNum</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	496 483 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	497 484 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	498 485 <span class="c"># Use complete sequence corresponding to reference sequence ID...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	499 486 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	500 487 <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">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	501 488 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	502 489 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	503 490 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="i">$RefereceSequenceLen</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	504 491 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	505 492 <span class="i">$RefereceSequenceRegionCount</span> = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	506 493 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	507 494 <span class="c"># Setup output file names...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	508 495 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	509 496 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	510 497 <span class="i">$FileExt</span> = <span class="q">"csv"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	511 498 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	512 499 <span class="i">$FileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	513 500 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	514 501 <span class="i">$OutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	515 502 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SequenceFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	516 503 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	517 504 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	518 505 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	519 506 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	520 507 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	521 508 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	522 509 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	523 510 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	524 511 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	525 512 <span class="k">else</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	526 513 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	527 514 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	528 515 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	529 516 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculatePercentIdentityMatrix</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	530 517 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}PercentIdentityMatrix.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	531 518 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	532 519 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	533 520 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	534 521 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	535 522 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	536 523 <span class="k">my</span><span class="s">(</span><span class="i">$RegionNum</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	537 524 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	538 525 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	539 526 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	540 527 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	541 528 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	542 529 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	543 530 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	544 531 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	545 532 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	546 533 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	547 534 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	548 535 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	549 536
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	550 537 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	551 538 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	552 539 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	553 540
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	554 541 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	555 542 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="i">$SequenceCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	556 543 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceID</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	557 544 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequence</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	558 545 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceLen</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	559 546 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceWithNoGaps</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	560 547 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	561 548 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	562 549 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceRegionCount</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	563 550
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	564 551 <span class="c"># Setup residue codes...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	565 552 <span class="i">SetupSequenceFileResidueCodes</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	566 553 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	567 554 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	568 555
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	569 <a name="SetupSequenceFileResidueCodes-"></a> 556 <span class="k">sub </span><span class="m">SetupSequenceFileResidueCodes</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	570 557 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	571 558 <span class="k">my</span><span class="s">(</span><span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	572 559
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	573 560 <span class="c"># Initialize</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	574 561 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	575 562
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	576 563 <span class="i">%ResidueCodesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	577 564 <span class="i">@ResidueCodesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	578 565
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	579 566 <span class="c"># Setup standard amino acids and nucleic acids one letter codes...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	580 567 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	581 568 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	582 569 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	583 570 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	584 571 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	585 572 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	586 573 <span class="k">push</span> <span class="i">@ResidueCodesList</span><span class="cm">,</span> <span class="q">'Gap'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	587 574 <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="i">@ResidueCodesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	588 575 <span class="i">$ResidueCodesMap</span>{<span class="i">$Residue</span>} = <span class="i">$Residue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	589 576 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	590 577
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	591 578 <span class="c"># Go over all the residues in all the sequences and add missing ones to the list...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	592 579 <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">$ResIndex</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	593 580 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	594 581 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	595 582 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	596 583 <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">$ResIndex</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	597 584 <span class="k">if</span> <span class="s">(</span><span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	598 585 <span class="k">next</span> <span class="j">RES</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	599 586 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	600 587 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	601 588 <span class="k">next</span> <span class="j">RES</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	602 589 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	603 590 <span class="k">push</span> <span class="i">@ResidueCodesList</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	604 591 <span class="i">$ResidueCodesMap</span>{<span class="i">$Residue</span>} = <span class="i">$Residue</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	605 592 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	606 593 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	607 594 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	608 595 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	609 596
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	610 597 <span class="c"># Setup regions data for performing residue frequency analysis...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	611 <a name="SetupSequenceRegionsData-"></a> 598 <span class="k">sub </span><span class="m">SetupSequenceRegionsData</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	612 599 <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">$ResidueCode</span><span class="cm">,</span> <span class="i">@RefereceSequenceRegions</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	613 600
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	614 601
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	615 602 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	616 603 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	617 604
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	618 605 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	619 606 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">IsGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	620 607 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">NoGapToGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	621 608 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">GapToNoGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	622 609 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	623 610 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]{<span class="w">RegionIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	624 611
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	625 612 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	626 613 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	627 614 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	628 615 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	629 616 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	630 617 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	631 618
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	632 619 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	633 620 <span class="i">$RefereceSequenceLen</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	634 621
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	635 622 <span class="c"># Setup residue number mapping and gap status for refernece sequence...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	636 623 <span class="i">$NoGapResNum</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	637 624 <span class="i">$ResNum</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	638 625 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	639 626 <span class="i">$ResNum</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	640 627 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	641 628 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">IsGap</span>}{<span class="i">$ResNum</span>} = <span class="n">1</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	642 629 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	643 630 <span class="i">$NoGapResNum</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	644 631 <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	645 632 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	646 633 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	647 634 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	648 635 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	649 636 <span class="c"># Map residue numbers for specified regions to the reference residue in input sequence/alignment files</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	650 637 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	651 638 <span class="i">@RefereceSequenceRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	652 639 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}[<span class="i">$Index</span>]}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	653 640 <span class="k">for</span> <span class="s">(</span><span class="i">$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">$RegionIndex</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	654 641 <span class="i">$StartResNum</span> = <span class="i">$RefereceSequenceRegions</span>[<span class="i">$RegionIndex</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	655 642 <span class="i">$EndResNum</span> = <span class="i">$RefereceSequenceRegions</span>[<span class="i">$RegionIndex</span> + <span class="n">1</span>]<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	656 643 <span class="i">$RegionNum</span>++<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	657 644 <span class="i">$RegionID</span> = <span class="q">"Region${RegionNum}"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	658 645 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	659 646 <span class="c"># Map residue numbers to the reference sequence residue numbers to account for any ignored gaps...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	660 647 <span class="i">$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">$StartResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	661 648 <span class="i">$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">$EndResNum</span>}<span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	662 649 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	663 650 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	664 651 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	665 652 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	666 653
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	667 654 <span class="c"># Initialize data for residue codes...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	668 655 <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	669 656 <span class="k">for</span> <span class="i">$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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	670 657 <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">$ResidueCode</span>} = <span class="n">0</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	671 658 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	672 659 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	673 660 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	674 661 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	675 662 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	676 663
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	677 664 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	678 <a name="SetupScriptUsage-"></a> 665 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	679 666
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	680 667 <span class="c"># Retrieve all the options...</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	681 668 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	682 669 <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">'yes'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	683 670 <span class="i">$Options</span>{<span class="w">regionresiduesmode</span>} = <span class="q">'None'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	684 671 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'PercentIdentityMatrix'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	685 672 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	686 673 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	687 674 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	688 675 <span class="i">$Options</span>{<span class="w">referencesequence</span>} = <span class="q">'UseFirstSequenceID'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	689 676 <span class="i">$Options</span>{<span class="w">region</span>} = <span class="q">'UseCompleteSequence'</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	690 677
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	691 678 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help\|h"</span><span class="cm">,</span> <span class="q">"ignoregaps\|i=s"</span><span class="cm">,</span> <span class="q">"mode\|m=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"overwrite\|o"</span><span class="cm">,</span> <span class="q">"precision\|p=i"</span><span class="cm">,</span> <span class="q">"quote\|q=s"</span><span class="cm">,</span> <span class="q">"referencesequence=s"</span><span class="cm">,</span> <span class="q">"region=s"</span><span class="cm">,</span> <span class="q">"regionresiduesmode=s"</span><span class="cm">,</span> <span class="q">"root\|r=s"</span><span class="cm">,</span> <span class="q">"workingdir\|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	692 679 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	693 680 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	694 681 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	695 682 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	696 683 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	697 684 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	698 685 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	699 686 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	700 687 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes\|no)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	701 688 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ignoregaps}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	702 689 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	703 690 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">regionresiduesmode</span>} !~ <span class="q">/^(AminoAcids\|NucleicAcids\|None)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	704 691 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{regionresiduesmode}, for option \"--regionresiduesmode\" is not valid. Allowed values: AminoAcids, NucleicAcids or None\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	705 692 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	706 693 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(PercentIdentityMatrix\|ResidueFrequencyAnalysis\|All)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	707 694 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: PercentIdentityMatrix, ResidueFrequencyAnalysis or All\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	708 695 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	709 696 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma\|semicolon\|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	710 697 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	711 698 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	712 699 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes\|no)$/i</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	713 700 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	714 701 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	715 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	716 703 <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>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	717 704 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	718 705 <span class="s">}</span>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	719 706
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	720 <a name="EOF-"></a></pre>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	721 <p> </p>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	722 <br />
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	723 <center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	724 <img src="../../../images/h2o2.png">
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	725 </center>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	726 </body>
4816e4a8ae95 Uploaded deepakjadmin parents: diff changeset	727 </html>

Mercurial > repos > deepakjadmin > mayatool3_test2

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