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comparison mayachemtools/docs/scripts/html/code/AnalyzeSequenceFilesData.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:AnalyzeSequenceFilesData.pl</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 1 #!/usr/bin/perl -w | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: AnalyzeSequenceFilesData.pl,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:46:04 $</span> | |
| 18 5 <span class="c"># $Revision: 1.33 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">NucleicAcids</span><span class="sc">;</span> | |
| 53 40 | |
| 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> | |
| 55 42 | |
| 56 43 <span class="c"># Autoflush STDOUT</span> | |
| 57 44 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> | |
| 58 45 | |
| 59 46 <span class="c"># Starting message...</span> | |
| 60 47 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> | |
| 61 48 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> | |
| 62 49 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 63 50 | |
| 64 51 <span class="c"># Setup script usage message...</span> | |
| 65 52 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 66 53 <span class="k">if</span> <span class="s">(</span><span class="i">$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> | |
| 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> | |
| 68 55 <span class="s">}</span> | |
| 69 56 | |
| 70 57 <span class="c"># Expand wild card file names...</span> | |
| 71 58 <span class="k">my</span><span class="s">(</span><span class="i">@SequenceFilesList</span><span class="s">)</span><span class="sc">;</span> | |
| 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> | |
| 73 60 | |
| 74 61 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> | |
| 75 62 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> | |
| 76 63 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 77 64 | |
| 78 65 <span class="c"># Set up information about input files...</span> | |
| 79 66 <span class="k">print</span> <span class="q">"Checking input sequence file(s)...\n"</span><span class="sc">;</span> | |
| 80 67 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span> | |
| 81 68 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 82 69 <span class="i">SetupSequenceRegionsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 83 70 | |
| 84 71 <span class="c"># Process input files..</span> | |
| 85 72 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 86 73 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 87 74 <span class="k">print</span> <span class="q">"\nProcessing sequence files...\n"</span><span class="sc">;</span> | |
| 88 75 <span class="s">}</span> | |
| 89 76 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span> | |
| 90 77 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> | |
| 91 78 <span class="k">print</span> <span class="q">"\nProcessing file $SequenceFilesList[$FileIndex]...\n"</span><span class="sc">;</span> | |
| 92 79 <span class="i">AnalyzeSequenceFileData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 93 80 <span class="s">}</span> | |
| 94 81 <span class="s">}</span> | |
| 95 82 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> | |
| 96 83 | |
| 97 84 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> | |
| 98 85 <span class="i">$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> | |
| 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> | |
| 100 87 | |
| 101 88 <span class="c">###############################################################################</span> | |
| 102 89 | |
| 103 90 <span class="c"># Analyze sequence file...</span> | |
| 104 <a name="AnalyzeSequenceFileData-"></a> 91 <span class="k">sub </span><span class="m">AnalyzeSequenceFileData</span> <span class="s">{</span> | |
| 105 92 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 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> | |
| 107 94 | |
| 108 95 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 109 96 | |
| 110 97 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $SequenceFile: $! \n"</span><span class="sc">;</span> | |
| 111 98 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 112 99 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> | |
| 113 100 | |
| 114 101 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculatePercentIdentityMatrix</span>}<span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 116 103 <span class="s">}</span> | |
| 117 104 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span> | |
| 118 105 <span class="i">PerformResidueFrequencyAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> | |
| 119 106 <span class="s">}</span> | |
| 120 107 <span class="s">}</span> | |
| 121 108 | |
| 122 109 <span class="c"># Calculate percent identity matrix...</span> | |
| 123 <a name="CalculatePercentIdentityMatrix-"></a> 110 <span class="k">sub </span><span class="m">CalculatePercentIdentityMatrix</span> <span class="s">{</span> | |
| 124 111 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 125 112 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> | |
| 126 113 | |
| 127 114 <span class="i">$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> | |
| 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> | |
| 129 116 | |
| 130 117 <span class="k">print</span> <span class="q">"Generating percent identity matrix file $PercentIdentityMatrixFile...\n"</span><span class="sc">;</span> | |
| 131 118 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$PercentIdentityMatrixFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Can't open $PercentIdentityMatrixFile: $!\n"</span><span class="sc">;</span> | |
| 132 119 | |
| 133 120 <span class="c"># Write out column labels...</span> | |
| 134 121 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 135 122 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span> | |
| 136 123 <span class="k">for</span> <span class="i">$ColID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 137 124 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ColID</span><span class="sc">;</span> | |
| 138 125 <span class="s">}</span> | |
| 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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> | |
| 140 127 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 141 128 | |
| 142 129 <span class="c"># Write out rows...</span> | |
| 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> | |
| 144 131 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 145 132 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$RowID</span><span class="sc">;</span> | |
| 146 133 <span class="k">for</span> <span class="i">$ColID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 147 134 <span class="i">$PercentIdentity</span> = <span class="i">$PercentIdentityMatrixRef</span>->{<span class="w">PercentIdentity</span>}{<span class="i">$RowID</span>}{<span class="i">$ColID</span>}<span class="sc">;</span> | |
| 148 135 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$PercentIdentity</span><span class="sc">;</span> | |
| 149 136 <span class="s">}</span> | |
| 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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> | |
| 151 138 <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 152 139 <span class="s">}</span> | |
| 153 140 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> | |
| 154 141 <span class="s">}</span> | |
| 155 142 | |
| 156 143 <span class="c"># Perform frequency analysis...</span> | |
| 157 <a name="PerformResidueFrequencyAnalysis-"></a> 144 <span class="k">sub </span><span class="m">PerformResidueFrequencyAnalysis</span> <span class="s">{</span> | |
| 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> | |
| 159 146 | |
| 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> | |
| 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> | |
| 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> | |
| 163 150 <span class="s">}</span> | |
| 164 151 | |
| 165 152 <span class="c"># Count residues...</span> | |
| 166 <a name="CountResiduesInRegions-"></a> 153 <span class="k">sub </span><span class="m">CountResiduesInRegions</span> <span class="s">{</span> | |
| 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> | |
| 168 155 | |
| 169 156 <span class="c"># Setup rerfernce sequence data...</span> | |
| 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> | |
| 171 158 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 172 159 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 173 160 | |
| 174 161 <span class="c"># Count residues...</span> | |
| 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> | |
| 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">$FileIndex</span>]{<span class="w">RegionIDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 177 164 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span> | |
| 178 165 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span> | |
| 179 166 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> | |
| 180 167 <span class="i">$ResIndex</span> = <span class="i">$ResNum</span> - <span class="n">1</span><span class="sc">;</span> | |
| 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> | |
| 182 169 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> | |
| 183 170 <span class="s">}</span> | |
| 184 171 <span class="c"># Go over residues in column $ResNum in all the sequences...</span> | |
| 185 172 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 186 173 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 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">$ResIndex</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 188 175 <span class="k">if</span> <span class="s">(</span><span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 190 177 <span class="s">}</span> | |
| 191 178 <span class="k">else</span> <span class="s">{</span> | |
| 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">$Residue</span>}<span class="s">)</span> <span class="s">{</span> | |
| 193 180 <span class="i">$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> | |
| 194 181 <span class="s">}</span> | |
| 195 182 <span class="k">else</span> <span class="s">{</span> | |
| 196 183 <span class="c"># Internal error...</span> | |
| 197 184 <span class="k">print</span> <span class="q">"Warning: Ignoring residue $Residue in sequence $ID during ResidueFrequencyAnalysis calculation: Unknown residue...\n"</span><span class="sc">;</span> | |
| 198 185 <span class="s">}</span> | |
| 199 186 <span class="s">}</span> | |
| 200 187 <span class="s">}</span> | |
| 201 188 <span class="s">}</span> | |
| 202 189 <span class="s">}</span> | |
| 203 190 <span class="s">}</span> | |
| 204 191 | |
| 205 192 <span class="c"># Calculate percent frequency for various residues in the sequence regions...</span> | |
| 206 <a name="CalculatePercentResidueFrequencyInRegions-"></a> 193 <span class="k">sub </span><span class="m">CalculatePercentResidueFrequencyInRegions</span> <span class="s">{</span> | |
| 207 194 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 208 195 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 209 196 | |
| 210 197 <span class="i">$MaxResiduesCount</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span> | |
| 211 198 <span class="i">$Precision</span> = <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="sc">;</span> | |
| 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">$FileIndex</span>]{<span class="w">RegionIDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 213 200 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span> | |
| 214 201 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span> | |
| 215 202 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 217 204 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> | |
| 218 205 <span class="s">}</span> | |
| 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">$ResNum</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 220 207 <span class="i">$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">$Residue</span>}<span class="sc">;</span> | |
| 221 208 <span class="i">$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> | |
| 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">$PercentCount</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
| 223 210 <span class="i">$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">$PercentCount</span><span class="sc">;</span> | |
| 224 211 <span class="s">}</span> | |
| 225 212 <span class="s">}</span> | |
| 226 213 <span class="s">}</span> | |
| 227 214 <span class="s">}</span> | |
| 228 215 | |
| 229 216 <span class="c"># Generate output files...</span> | |
| 230 <a name="GeneratePercentResidueFrequencyOutFilesForRegions-"></a> 217 <span class="k">sub </span><span class="m">GeneratePercentResidueFrequencyOutFilesForRegions</span> <span class="s">{</span> | |
| 231 218 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 232 219 | |
| 233 220 <span class="c"># Setup rerfernce sequence data...</span> | |
| 234 221 <span class="k">my</span><span class="s">(</span><span class="i">$RefereceSequenceID</span><span class="cm">,</span> <span class="i">$RefereceSequence</span><span class="s">)</span><span class="sc">;</span> | |
| 235 222 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 236 223 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 237 224 | |
| 238 225 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 239 226 | |
| 240 227 <span class="i">$OutFileRoot</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 241 228 <span class="i">$OutFileExt</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> | |
| 242 229 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 243 230 <span class="k">for</span> <span class="i">$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> | |
| 244 231 <span class="i">$RegionNum</span>++<span class="sc">;</span> | |
| 245 232 <span class="i">$StartResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">StartResNum</span>}<span class="sc">;</span> | |
| 246 233 <span class="i">$EndResNum</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$FileIndex</span>]{<span class="i">$RegionID</span>}{<span class="w">EndResNum</span>}<span class="sc">;</span> | |
| 247 234 | |
| 248 235 <span class="i">$RegionOutFile</span> = <span class="q">"${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="sc">;</span> | |
| 249 236 <span class="i">$PercentRegionOutFile</span> = <span class="q">"${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="sc">;</span> | |
| 250 237 | |
| 251 238 <span class="k">print</span> <span class="q">"Generating $RegionOutFile and $PercentRegionOutFile...\n"</span><span class="sc">;</span> | |
| 252 239 <span class="k">open</span> <span class="w">REGIONOUTFILE</span><span class="cm">,</span> <span class="q">">$RegionOutFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $RegionOutFile: $! \n"</span><span class="sc">;</span> | |
| 253 240 <span class="k">open</span> <span class="w">PERCENTREGIONOUTFILE</span><span class="cm">,</span> <span class="q">">$PercentRegionOutFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $PercentRegionOutFile: $! \n"</span><span class="sc">;</span> | |
| 254 241 | |
| 255 242 <span class="c"># Write out reference residue positions as column values....</span> | |
| 256 243 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 257 244 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span> | |
| 258 245 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 260 247 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> | |
| 261 248 <span class="s">}</span> | |
| 262 249 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$ResNum</span><span class="sc">;</span> | |
| 263 250 <span class="s">}</span> | |
| 264 251 <span class="i">$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> | |
| 265 252 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 266 253 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 267 254 | |
| 268 255 | |
| 269 256 <span class="c"># Write out row data for each residue; Gap residue is written last...</span> | |
| 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">$FileIndex</span>]}<span class="s">)</span> <span class="s">{</span> | |
| 271 258 <span class="k">if</span> <span class="s">(</span><span class="i">$Residue</span> =~ <span class="q">/^Gap$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 272 259 <span class="k">next</span> <span class="j">RESIDUE</span><span class="sc">;</span> | |
| 273 260 <span class="s">}</span> | |
| 274 261 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 275 262 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> | |
| 276 263 <span class="i">@PercentLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 277 264 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> | |
| 278 265 | |
| 279 266 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 281 268 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> | |
| 282 269 <span class="s">}</span> | |
| 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> | |
| 284 271 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Count</span><span class="sc">;</span> | |
| 285 272 <span class="i">$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">$Residue</span>}<span class="sc">;</span> | |
| 286 273 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="sc">;</span> | |
| 287 274 <span class="s">}</span> | |
| 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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> | |
| 289 276 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 290 277 | |
| 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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> | |
| 292 279 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 293 280 <span class="s">}</span> | |
| 294 281 | |
| 295 282 <span class="c"># Write out data for gap...</span> | |
| 296 283 <span class="i">$Residue</span> = <span class="q">'Gap'</span><span class="sc">;</span> | |
| 297 284 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 298 285 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> | |
| 299 286 <span class="i">@PercentLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 300 287 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> | |
| 301 288 | |
| 302 289 <span class="j">RESNUM:</span> <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 304 291 <span class="k">next</span> <span class="j">RESNUM</span><span class="sc">;</span> | |
| 305 292 <span class="s">}</span> | |
| 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> | |
| 307 294 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$Count</span><span class="sc">;</span> | |
| 308 295 | |
| 309 296 <span class="i">$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">$Residue</span>}<span class="sc">;</span> | |
| 310 297 <span class="k">push</span> <span class="i">@PercentLineWords</span><span class="cm">,</span> <span class="i">$PercentCount</span><span class="sc">;</span> | |
| 311 298 <span class="s">}</span> | |
| 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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> | |
| 313 300 <span class="k">print</span> <span class="i">REGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 314 301 | |
| 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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> | |
| 316 303 <span class="k">print</span> <span class="i">PERCENTREGIONOUTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span> | |
| 317 304 | |
| 318 305 <span class="k">close</span> <span class="w">REGIONOUTFILE</span><span class="sc">;</span> | |
| 319 306 <span class="k">close</span> <span class="w">PERCENTREGIONOUTFILE</span><span class="sc">;</span> | |
| 320 307 <span class="s">}</span> | |
| 321 308 <span class="s">}</span> | |
| 322 309 | |
| 323 310 <span class="c"># Process option values...</span> | |
| 324 <a name="ProcessOptions-"></a> 311 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> | |
| 325 312 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 326 313 | |
| 327 314 <span class="c"># Setup analysis mode...</span> | |
| 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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 329 316 <span class="i">$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> | |
| 330 317 | |
| 331 318 <span class="c"># Setup delimiter and quotes...</span> | |
| 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">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span> | |
| 333 320 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/yes/i</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 334 321 | |
| 335 322 <span class="c"># Setup reference sequence and regions for residue frequence analysis...</span> | |
| 336 323 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRefereceSequence</span>} = <span class="i">$Options</span>{<span class="w">referencesequence</span>}<span class="sc">;</span> | |
| 337 324 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegion</span>} = <span class="i">$Options</span>{<span class="w">region</span>}<span class="sc">;</span> | |
| 338 325 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 339 326 | |
| 340 327 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedRegions</span><span class="s">)</span><span class="sc">;</span> | |
| 341 328 <span class="i">@SpecifiedRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 342 329 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">region</span>} =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span> | |
| 343 330 <span class="i">@SpecifiedRegions</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegion</span>}<span class="sc">;</span> | |
| 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> | |
| 345 332 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"</span><span class="sc">;</span> | |
| 346 333 <span class="s">}</span> | |
| 347 334 <span class="c"># Make sure EndResNum > StartResNum...</span> | |
| 348 335 <span class="k">my</span><span class="s">(</span><span class="i">$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">$RegionNum</span><span class="s">)</span><span class="sc">;</span> | |
| 349 336 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 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> | |
| 351 338 <span class="i">$StartResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 352 339 <span class="i">$EndResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 353 340 <span class="i">$RegionNum</span>++<span class="sc">;</span> | |
| 354 341 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$StartResNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 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 $RegionNum.\n"</span><span class="sc">;</span> | |
| 356 343 <span class="s">}</span> | |
| 357 344 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$EndResNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 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 $RegionNum.\n"</span><span class="sc">;</span> | |
| 359 346 <span class="s">}</span> | |
| 360 347 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> >= <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> | |
| 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 $RegionNum.\n"</span><span class="sc">;</span> | |
| 362 349 <span class="s">}</span> | |
| 363 350 <span class="s">}</span> | |
| 364 351 <span class="s">}</span> | |
| 365 352 <span class="k">else</span> <span class="s">{</span> | |
| 366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">region</span>} !~ <span class="q">/^UseCompleteSequence$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 367 354 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{region}, for option \"--region\" is not valid. Allowed values: \"StartResNum,EndResNum,[StartResNum,EndResNum...]\" or UseCompleteSequence\n"</span><span class="sc">;</span> | |
| 368 355 <span class="s">}</span> | |
| 369 356 <span class="s">}</span> | |
| 370 357 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}}<span class="cm">,</span> <span class="i">@SpecifiedRegions</span><span class="sc">;</span> | |
| 371 358 | |
| 372 359 <span class="c"># Miscellaneous options...</span> | |
| 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> | |
| 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> | |
| 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> | |
| 376 363 | |
| 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> | |
| 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">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 379 366 <span class="s">}</span> | |
| 380 367 | |
| 381 368 <span class="c"># Retrieve information about sequence files...</span> | |
| 382 <a name="RetrieveSequenceFilesInfo-"></a> 369 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span> | |
| 383 370 <span class="k">my</span><span class="s">(</span><span class="i">$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">$SpecifiedRefereceSequence</span><span class="cm">,</span> <span class="i">@SpecifiedRegions</span><span class="cm">,</span> <span class="i">@RefereceSequenceRegions</span><span class="s">)</span><span class="sc">;</span> | |
| 384 371 | |
| 385 372 <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 386 373 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 387 374 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 388 375 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 389 376 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 390 377 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 391 378 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 392 379 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 393 380 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 394 381 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 395 382 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 396 383 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 397 384 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 398 385 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 399 386 | |
| 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> | |
| 401 388 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 402 389 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> | |
| 403 390 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 404 391 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 405 392 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="q">'NotSupported'</span><span class="sc">;</span> | |
| 406 393 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> | |
| 407 394 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 408 395 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 409 396 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 410 397 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 411 398 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> | |
| 412 399 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 413 400 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> | |
| 414 401 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">ResidueCodes</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 415 402 | |
| 416 403 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span><span class="s">)</span> <span class="s">{</span> | |
| 417 404 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n"</span><span class="sc">;</span> | |
| 418 405 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 419 406 <span class="s">}</span> | |
| 420 407 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> | |
| 421 408 | |
| 422 409 <span class="s">(</span><span class="i">$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> | |
| 423 410 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span> | |
| 424 411 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n"</span><span class="sc">;</span> | |
| 425 412 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 426 413 <span class="s">}</span> | |
| 427 414 | |
| 428 415 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> | |
| 429 416 | |
| 430 417 <span class="i">$SequenceCount</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span> | |
| 431 418 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceCount</span><span class="s">)</span> <span class="s">{</span> | |
| 432 419 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence data is missing.\n"</span><span class="sc">;</span> | |
| 433 420 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 434 421 <span class="s">}</span> | |
| 435 422 | |
| 436 423 <span class="c"># Make sure all sequence lengths are identical...</span> | |
| 437 424 <span class="k">if</span> <span class="s">(</span>!<span class="i">AreSequenceLengthsIdentical</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 438 425 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence legths are not identical.\n"</span><span class="sc">;</span> | |
| 439 426 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 440 427 <span class="s">}</span> | |
| 441 428 <span class="i">$SpecifiedRefereceSequence</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRefereceSequence</span>}<span class="sc">;</span> | |
| 442 429 <span class="c"># Make sure reference sequence ID is valid...</span> | |
| 443 430 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRefereceSequence</span> =~ <span class="q">/^UseFirstSequenceID$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 444 431 <span class="i">$RefereceSequenceID</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span> | |
| 445 432 <span class="s">}</span> | |
| 446 433 <span class="k">else</span> <span class="s">{</span> | |
| 447 434 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$SpecifiedRefereceSequence</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 448 435 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Rreference sequence ID, $SpecifiedRefereceSequence, specified using option \"--referencesequence\" is missing.\n"</span><span class="sc">;</span> | |
| 449 436 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 450 437 <span class="s">}</span> | |
| 451 438 <span class="i">$RefereceSequenceID</span> = <span class="i">$SpecifiedRefereceSequence</span><span class="sc">;</span> | |
| 452 439 <span class="s">}</span> | |
| 453 440 | |
| 454 441 <span class="c"># Make sure sequence regions corresponding to reference sequence are valid...</span> | |
| 455 442 <span class="i">@RefereceSequenceRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 456 443 <span class="i">$RefereceSequenceRegionCount</span> = <span class="n">0</span><span class="sc">;</span> | |
| 457 444 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$RefereceSequenceID</span>}<span class="sc">;</span> | |
| 458 445 <span class="i">$RefereceSequenceLen</span> = <span class="k">length</span> <span class="i">$RefereceSequence</span><span class="sc">;</span> | |
| 459 446 | |
| 460 447 <span class="i">$RefereceSequenceWithNoGaps</span> = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$RefereceSequence</span><span class="s">)</span><span class="sc">;</span> | |
| 461 448 <span class="i">$RefereceSequenceWithNoGapsLen</span> = <span class="k">length</span> <span class="i">$RefereceSequenceWithNoGaps</span><span class="sc">;</span> | |
| 462 449 | |
| 463 450 <span class="i">@SpecifiedRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 464 451 <span class="k">push</span> <span class="i">@SpecifiedRegions</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedRegions</span>}}<span class="sc">;</span> | |
| 465 452 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedRegions</span><span class="s">)</span> <span class="s">{</span> | |
| 466 453 <span class="c"># Make sure specified regions are valid...</span> | |
| 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> | |
| 468 455 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 469 456 <span class="k">for</span> <span class="s">(</span><span class="i">$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">$RegionIndex</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 470 457 <span class="i">$StartResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$RegionIndex</span>]<span class="sc">;</span> | |
| 471 458 <span class="i">$EndResNum</span> = <span class="i">$SpecifiedRegions</span>[<span class="i">$RegionIndex</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 472 459 <span class="i">$RegionNum</span>++<span class="sc">;</span> | |
| 473 460 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span> | |
| 474 461 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> > <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span> <span class="s">{</span> | |
| 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 $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"</span><span class="sc">;</span> | |
| 476 463 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 477 464 <span class="s">}</span> | |
| 478 465 <span class="k">if</span> <span class="s">(</span><span class="i">$EndResNum</span> > <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span> <span class="s">{</span> | |
| 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 $RegionNum. The reference sequence residue numbers correspond to the sequence with no gaps. Specify \"No\" value for \"-i, --ignoregaps\" option to use residue numbers corresponding to reference sequence including gaps.\n"</span><span class="sc">;</span> | |
| 480 467 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 481 468 <span class="s">}</span> | |
| 482 469 <span class="s">}</span> | |
| 483 470 <span class="k">else</span> <span class="s">{</span> | |
| 484 471 <span class="k">if</span> <span class="s">(</span><span class="i">$StartResNum</span> > <span class="i">$RefereceSequenceLen</span><span class="s">)</span> <span class="s">{</span> | |
| 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 $RegionNum.\n"</span><span class="sc">;</span> | |
| 486 473 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 487 474 <span class="s">}</span> | |
| 488 475 <span class="k">if</span> <span class="s">(</span><span class="i">$EndResNum</span> > <span class="i">$RefereceSequenceLen</span><span class="s">)</span> <span class="s">{</span> | |
| 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 $RegionNum.\n"</span><span class="sc">;</span> | |
| 490 477 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 491 478 <span class="s">}</span> | |
| 492 479 <span class="s">}</span> | |
| 493 480 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="s">(</span><span class="i">$StartResNum</span><span class="cm">,</span> <span class="i">$EndResNum</span><span class="s">)</span><span class="sc">;</span> | |
| 494 481 <span class="s">}</span> | |
| 495 482 <span class="i">$RefereceSequenceRegionCount</span> = <span class="i">$RegionNum</span><span class="sc">;</span> | |
| 496 483 <span class="s">}</span> | |
| 497 484 <span class="k">else</span> <span class="s">{</span> | |
| 498 485 <span class="c"># Use complete sequence corresponding to reference sequence ID...</span> | |
| 499 486 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span> | |
| 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">$RefereceSequenceWithNoGapsLen</span><span class="s">)</span><span class="sc">;</span> | |
| 501 488 <span class="s">}</span> | |
| 502 489 <span class="k">else</span> <span class="s">{</span> | |
| 503 490 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="s">(</span><span class="n">1</span><span class="cm">,</span> <span class="i">$RefereceSequenceLen</span><span class="s">)</span><span class="sc">;</span> | |
| 504 491 <span class="s">}</span> | |
| 505 492 <span class="i">$RefereceSequenceRegionCount</span> = <span class="n">1</span><span class="sc">;</span> | |
| 506 493 <span class="s">}</span> | |
| 507 494 <span class="c"># Setup output file names...</span> | |
| 508 495 <span class="i">$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> | |
| 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> | |
| 510 497 <span class="i">$FileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> | |
| 511 498 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 512 499 <span class="i">$FileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> | |
| 513 500 <span class="s">}</span> | |
| 514 501 <span class="i">$OutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span> | |
| 515 502 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SequenceFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 516 503 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> | |
| 517 504 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> | |
| 518 505 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> | |
| 519 506 <span class="s">}</span> | |
| 520 507 <span class="k">else</span> <span class="s">{</span> | |
| 521 508 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> | |
| 522 509 <span class="s">}</span> | |
| 523 510 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> | |
| 524 511 <span class="s">}</span> | |
| 525 512 <span class="k">else</span> <span class="s">{</span> | |
| 526 513 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> | |
| 527 514 <span class="s">}</span> | |
| 528 515 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> | |
| 529 516 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CalculatePercentIdentityMatrix</span>}<span class="s">)</span> <span class="s">{</span> | |
| 530 517 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}PercentIdentityMatrix.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 532 519 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 533 520 <span class="s">}</span> | |
| 534 521 <span class="s">}</span> | |
| 535 522 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span> | |
| 536 523 <span class="k">my</span><span class="s">(</span><span class="i">$RegionNum</span><span class="s">)</span><span class="sc">;</span> | |
| 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> | |
| 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> | |
| 539 526 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}ResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"</span><span class="sc">;</span> | |
| 540 527 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 541 528 <span class="s">}</span> | |
| 542 529 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> | |
| 543 530 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}PercentResidueFrequencyAnalysisRegion${RegionNum}.${OutFileExt} already exists\n"</span><span class="sc">;</span> | |
| 544 531 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 545 532 <span class="s">}</span> | |
| 546 533 <span class="s">}</span> | |
| 547 534 <span class="s">}</span> | |
| 548 535 <span class="s">}</span> | |
| 549 536 | |
| 550 537 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> | |
| 551 538 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> | |
| 552 539 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span> | |
| 553 540 | |
| 554 541 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span> | |
| 555 542 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="i">$SequenceCount</span><span class="sc">;</span> | |
| 556 543 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceID</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceID</span><span class="sc">;</span> | |
| 557 544 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequence</span><span class="sc">;</span> | |
| 558 545 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceLen</span><span class="sc">;</span> | |
| 559 546 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGaps</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceWithNoGaps</span><span class="sc">;</span> | |
| 560 547 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceWithNoGapsLen</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceWithNoGapsLen</span><span class="sc">;</span> | |
| 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> | |
| 562 549 <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegionCount</span>}[<span class="i">$Index</span>] = <span class="i">$RefereceSequenceRegionCount</span><span class="sc">;</span> | |
| 563 550 | |
| 564 551 <span class="c"># Setup residue codes...</span> | |
| 565 552 <span class="i">SetupSequenceFileResidueCodes</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span> | |
| 566 553 <span class="s">}</span> | |
| 567 554 <span class="s">}</span> | |
| 568 555 | |
| 569 <a name="SetupSequenceFileResidueCodes-"></a> 556 <span class="k">sub </span><span class="m">SetupSequenceFileResidueCodes</span> <span class="s">{</span> | |
| 570 557 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 571 558 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 572 559 | |
| 573 560 <span class="c"># Initialize</span> | |
| 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> | |
| 575 562 | |
| 576 563 <span class="i">%ResidueCodesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 577 564 <span class="i">@ResidueCodesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 578 565 | |
| 579 566 <span class="c"># Setup standard amino acids and nucleic acids one letter codes...</span> | |
| 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> | |
| 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> | |
| 582 569 <span class="s">}</span> | |
| 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> | |
| 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> | |
| 585 572 <span class="s">}</span> | |
| 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> | |
| 587 574 <span class="k">for</span> <span class="i">$Residue</span> <span class="s">(</span><span class="i">@ResidueCodesList</span><span class="s">)</span> <span class="s">{</span> | |
| 588 575 <span class="i">$ResidueCodesMap</span>{<span class="i">$Residue</span>} = <span class="i">$Residue</span><span class="sc">;</span> | |
| 589 576 <span class="s">}</span> | |
| 590 577 | |
| 591 578 <span class="c"># Go over all the residues in all the sequences and add missing ones to the list...</span> | |
| 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">$ResIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 593 580 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 594 581 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> | |
| 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> | |
| 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">$ResIndex</span><span class="cm">,</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> | |
| 597 584 <span class="k">if</span> <span class="s">(</span><span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 598 585 <span class="k">next</span> <span class="j">RES</span><span class="sc">;</span> | |
| 599 586 <span class="s">}</span> | |
| 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> | |
| 601 588 <span class="k">next</span> <span class="j">RES</span><span class="sc">;</span> | |
| 602 589 <span class="s">}</span> | |
| 603 590 <span class="k">push</span> <span class="i">@ResidueCodesList</span><span class="cm">,</span> <span class="i">$Residue</span><span class="sc">;</span> | |
| 604 591 <span class="i">$ResidueCodesMap</span>{<span class="i">$Residue</span>} = <span class="i">$Residue</span><span class="sc">;</span> | |
| 605 592 <span class="s">}</span> | |
| 606 593 <span class="s">}</span> | |
| 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> | |
| 608 595 <span class="s">}</span> | |
| 609 596 | |
| 610 597 <span class="c"># Setup regions data for performing residue frequency analysis...</span> | |
| 611 <a name="SetupSequenceRegionsData-"></a> 598 <span class="k">sub </span><span class="m">SetupSequenceRegionsData</span> <span class="s">{</span> | |
| 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">$ResidueCode</span><span class="cm">,</span> <span class="i">@RefereceSequenceRegions</span><span class="s">)</span><span class="sc">;</span> | |
| 613 600 | |
| 614 601 | |
| 615 602 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 616 603 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 617 604 | |
| 618 605 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span> | |
| 619 606 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">IsGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 620 607 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">NoGapToGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 621 608 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceResNums</span>}[<span class="i">$Index</span>]{<span class="w">GapToNoGap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 622 609 <span class="i">%</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 623 610 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RegionsData</span>}[<span class="i">$Index</span>]{<span class="w">RegionIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 624 611 | |
| 625 612 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> | |
| 626 613 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 627 614 <span class="s">}</span> | |
| 628 615 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">PerformResidueFrequencyAnalysis</span>}<span class="s">)</span> <span class="s">{</span> | |
| 629 616 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> | |
| 630 617 <span class="s">}</span> | |
| 631 618 | |
| 632 619 <span class="i">$RefereceSequence</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequence</span>}[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 633 620 <span class="i">$RefereceSequenceLen</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceLen</span>}[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 634 621 | |
| 635 622 <span class="c"># Setup residue number mapping and gap status for refernece sequence...</span> | |
| 636 623 <span class="i">$NoGapResNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 637 624 <span class="i">$ResNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 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> | |
| 639 626 <span class="i">$ResNum</span>++<span class="sc">;</span> | |
| 640 627 <span class="i">$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> | |
| 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">$ResNum</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 642 629 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsGapResidue</span><span class="s">(</span><span class="i">$Residue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 643 630 <span class="i">$NoGapResNum</span>++<span class="sc">;</span> | |
| 644 631 <span class="i">$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> | |
| 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> | |
| 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> | |
| 647 634 <span class="s">}</span> | |
| 648 635 <span class="s">}</span> | |
| 649 636 <span class="c"># Map residue numbers for specified regions to the reference residue in input sequence/alignment files</span> | |
| 650 637 <span class="i">$RegionNum</span> = <span class="n">0</span><span class="sc">;</span> | |
| 651 638 <span class="i">@RefereceSequenceRegions</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 652 639 <span class="k">push</span> <span class="i">@RefereceSequenceRegions</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">RefereceSequenceRegions</span>}[<span class="i">$Index</span>]}<span class="sc">;</span> | |
| 653 640 <span class="k">for</span> <span class="s">(</span><span class="i">$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">$RegionIndex</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 654 641 <span class="i">$StartResNum</span> = <span class="i">$RefereceSequenceRegions</span>[<span class="i">$RegionIndex</span>]<span class="sc">;</span> | |
| 655 642 <span class="i">$EndResNum</span> = <span class="i">$RefereceSequenceRegions</span>[<span class="i">$RegionIndex</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 656 643 <span class="i">$RegionNum</span>++<span class="sc">;</span> | |
| 657 644 <span class="i">$RegionID</span> = <span class="q">"Region${RegionNum}"</span><span class="sc">;</span> | |
| 658 645 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span> | |
| 659 646 <span class="c"># Map residue numbers to the reference sequence residue numbers to account for any ignored gaps...</span> | |
| 660 647 <span class="i">$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">$StartResNum</span>}<span class="sc">;</span> | |
| 661 648 <span class="i">$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">$EndResNum</span>}<span class="sc">;</span> | |
| 662 649 <span class="s">}</span> | |
| 663 650 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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> | |
| 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> | |
| 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> | |
| 666 653 | |
| 667 654 <span class="c"># Initialize data for residue codes...</span> | |
| 668 655 <span class="k">for</span> <span class="i">$ResNum</span> <span class="s">(</span><span class="i">$StartResNum</span> .. <span class="i">$EndResNum</span><span class="s">)</span> <span class="s">{</span> | |
| 669 656 <span class="k">for</span> <span class="i">$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> | |
| 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">$ResidueCode</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 671 658 <span class="s">}</span> | |
| 672 659 <span class="s">}</span> | |
| 673 660 <span class="s">}</span> | |
| 674 661 <span class="s">}</span> | |
| 675 662 <span class="s">}</span> | |
| 676 663 | |
| 677 664 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> | |
| 678 <a name="SetupScriptUsage-"></a> 665 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> | |
| 679 666 | |
| 680 667 <span class="c"># Retrieve all the options...</span> | |
| 681 668 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 682 669 <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">'yes'</span><span class="sc">;</span> | |
| 683 670 <span class="i">$Options</span>{<span class="w">regionresiduesmode</span>} = <span class="q">'None'</span><span class="sc">;</span> | |
| 684 671 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'PercentIdentityMatrix'</span><span class="sc">;</span> | |
| 685 672 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> | |
| 686 673 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span> | |
| 687 674 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span> | |
| 688 675 <span class="i">$Options</span>{<span class="w">referencesequence</span>} = <span class="q">'UseFirstSequenceID'</span><span class="sc">;</span> | |
| 689 676 <span class="i">$Options</span>{<span class="w">region</span>} = <span class="q">'UseCompleteSequence'</span><span class="sc">;</span> | |
| 690 677 | |
| 691 678 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"ignoregaps|i=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"precision|p=i"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"referencesequence=s"</span><span class="cm">,</span> <span class="q">"region=s"</span><span class="cm">,</span> <span class="q">"regionresiduesmode=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 692 679 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> | |
| 693 680 <span class="s">}</span> | |
| 694 681 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 696 683 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> | |
| 697 684 <span class="s">}</span> | |
| 698 685 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> | |
| 699 686 <span class="s">}</span> | |
| 700 687 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 701 688 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ignoregaps}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> | |
| 702 689 <span class="s">}</span> | |
| 703 690 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">regionresiduesmode</span>} !~ <span class="q">/^(AminoAcids|NucleicAcids|None)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 704 691 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{regionresiduesmode}, for option \"--regionresiduesmode\" is not valid. Allowed values: AminoAcids, NucleicAcids or None\n"</span><span class="sc">;</span> | |
| 705 692 <span class="s">}</span> | |
| 706 693 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(PercentIdentityMatrix|ResidueFrequencyAnalysis|All)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 707 694 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: PercentIdentityMatrix, ResidueFrequencyAnalysis or All\n"</span><span class="sc">;</span> | |
| 708 695 <span class="s">}</span> | |
| 709 696 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 710 697 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> | |
| 711 698 <span class="s">}</span> | |
| 712 699 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 713 700 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> | |
| 714 701 <span class="s">}</span> | |
| 715 702 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 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> | |
| 717 704 <span class="s">}</span> | |
| 718 705 <span class="s">}</span> | |
| 719 706 | |
| 720 <a name="EOF-"></a></pre> | |
| 721 <p> </p> | |
| 722 <br /> | |
| 723 <center> | |
| 724 <img src="../../../images/h2o2.png"> | |
| 725 </center> | |
| 726 </body> | |
| 727 </html> |