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<html> <head> <title>MayaChemTools:Code:ExtractFromSequenceFiles.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> 1 #!/usr/bin/perl -w 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: ExtractFromSequenceFiles.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span> 5 <span class="c"># $Revision: 1.23 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span> 38 39 <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> 40 41 <span class="c"># Autoflush STDOUT</span> 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 43 44 <span class="c"># Starting message...</span> 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 48 49 <span class="c"># Setup script usage message...</span> 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 51 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 52 <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> 53 <span class="s">}</span> 54 55 <span class="c"># Expand wild card file names...</span> 56 <span class="k">my</span><span class="s">(</span><span class="i">@SequenceFilesList</span><span class="s">)</span><span class="sc">;</span> 57 <span class="i">@SequenceFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"aln msf fasta fta pir"</span><span class="s">)</span><span class="sc">;</span> 58 59 <span class="c"># Process options...</span> 60 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 61 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 62 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 63 64 <span class="c"># Set up information about input files...</span> 65 <span class="k">print</span> <span class="q">"Checking input sequence file(s)...\n"</span><span class="sc">;</span> 66 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span> 67 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 68 69 <span class="c"># Process input files..</span> 70 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 71 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 72 <span class="k">print</span> <span class="q">"\nProcessing sequence files...\n"</span><span class="sc">;</span> 73 <span class="s">}</span> 74 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span> 75 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> 76 <span class="k">print</span> <span class="q">"\nProcessing file $SequenceFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 77 <span class="i">ExtractFromSequenceFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 78 <span class="s">}</span> 79 <span class="s">}</span> 80 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 81 82 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 83 <span class="i">$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> 84 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 85 86 <span class="c">###############################################################################</span> 87 88 <span class="c"># Extract from sequence files...</span> <a name="ExtractFromSequenceFiles-"></a> 89 <span class="k">sub </span><span class="m">ExtractFromSequenceFiles</span> <span class="s">{</span> 90 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 91 <span class="k">my</span><span class="s">(</span><span class="i">$OutSequenceFile</span><span class="cm">,</span> <span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="sc">;</span> 92 93 <span class="c"># Read sequence file...</span> 94 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 95 <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $SequenceFile: $! \n"</span><span class="sc">;</span> 96 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> 97 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> 98 99 <span class="i">$OutSequenceFile</span> = <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 100 <span class="k">print</span> <span class="q">"Generating sequence file $OutSequenceFile...\n"</span><span class="sc">;</span> 101 102 <span class="c"># Retrieve sequence data for specified sequences...</span> 103 <span class="i">$SpecifiedSequenceDataRef</span> = <span class="i">GetSpecifiedSequenceData</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> 104 105 <span class="c"># Handle gaps...</span> 106 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span> 107 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SpecifiedSequenceDataRef</span>->{<span class="w">IDs</span>}} > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 108 <span class="k">if</span> <span class="s">(</span><span class="i">AreSequenceLengthsIdentical</span><span class="s">(</span><span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 109 <span class="i">$SpecifiedSequenceDataRef</span> = <span class="i">RemoveSequenceAlignmentGapColumns</span><span class="s">(</span><span class="i">$SpecifiedSequenceDataRef</span><span class="s">)</span><span class="sc">;</span> 110 <span class="s">}</span> 111 <span class="s">}</span> 112 <span class="k">else</span> <span class="s">{</span> 113 <span class="c"># Remove the gaps from the sequence...</span> 114 <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="s">)</span><span class="sc">;</span> 115 <span class="i">$ID</span> = <span class="i">$SpecifiedSequenceDataRef</span>->{<span class="w">IDs</span>}[<span class="n">0</span>]<span class="sc">;</span> 116 <span class="i">$Sequence</span> = <span class="i">$SpecifiedSequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 117 <span class="i">$SpecifiedSequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span> 118 <span class="s">}</span> 119 <span class="s">}</span> 120 121 <span class="c"># Write out the file...</span> 122 <span class="i">WritePearsonFastaSequenceFile</span><span class="s">(</span><span class="i">$OutSequenceFile</span><span class="cm">,</span> <span class="i">$SpecifiedSequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>}<span class="s">)</span><span class="sc">;</span> 123 <span class="s">}</span> 124 125 <span class="c"># Get specified sequence data...</span> <a name="GetSpecifiedSequenceData-"></a> 126 <span class="k">sub </span><span class="m">GetSpecifiedSequenceData</span> <span class="s">{</span> 127 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 128 129 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span> 130 <span class="k">return</span> <span class="i">GetDataBySequenceIDs</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> 131 <span class="s">}</span> 132 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span> 133 <span class="k">return</span> <span class="i">GetDataBySequenceNums</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> 134 <span class="s">}</span> 135 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span> 136 <span class="k">return</span> <span class="i">GetDataBySequenceNumRange</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> 137 <span class="s">}</span> 138 <span class="k">else</span> <span class="s">{</span> 139 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 140 <span class="s">}</span> 141 <span class="s">}</span> 142 143 <span class="c"># Get specified sequence data...</span> <a name="GetDataBySequenceIDs-"></a> 144 <span class="k">sub </span><span class="m">GetDataBySequenceIDs</span> <span class="s">{</span> 145 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 146 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">$IDMatched</span><span class="cm">,</span> <span class="i">$SpecifiedID</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span> 147 148 <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span> 149 <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 150 <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 151 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 152 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 153 154 <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span> 155 <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> 156 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">MatchExactSequenceIDs</span>}<span class="s">)</span> <span class="s">{</span> 157 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$ID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 158 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> 159 <span class="s">}</span> 160 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceCount</span> >= <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span> 161 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span> 162 <span class="s">}</span> 163 <span class="i">$SequenceCount</span>++<span class="sc">;</span> 164 <span class="s">}</span> 165 <span class="k">else</span> <span class="s">{</span> 166 <span class="c"># Does this ID contains specified ID as substring...</span> 167 <span class="i">$IDMatched</span> = <span class="n">0</span><span class="sc">;</span> 168 <span class="j">SPECIFIEDID:</span> <span class="k">for</span> <span class="i">$SpecifiedID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span> 169 <span class="k">if</span> <span class="s">(</span><span class="i">$ID</span> =~ <span class="q">/$SpecifiedID/i</span><span class="s">)</span> <span class="s">{</span> 170 <span class="i">$IDMatched</span> = <span class="n">1</span><span class="sc">;</span> 171 <span class="k">last</span> <span class="j">SPECIFIEDID</span><span class="sc">;</span> 172 <span class="s">}</span> 173 <span class="s">}</span> 174 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IDMatched</span><span class="s">)</span> <span class="s">{</span> 175 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> 176 <span class="s">}</span> 177 <span class="i">$SequenceCount</span>++<span class="sc">;</span> 178 <span class="s">}</span> 179 <span class="c"># Collect sequence data...</span> 180 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> 181 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>->{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 182 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 183 <span class="s">}</span> 184 185 <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span> 186 <span class="s">}</span> 187 188 <span class="c"># Get specified sequence data...</span> <a name="GetDataBySequenceNums-"></a> 189 <span class="k">sub </span><span class="m">GetDataBySequenceNums</span> <span class="s">{</span> 190 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 191 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceNum</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span> 192 193 <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span> 194 <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 195 <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 196 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 197 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 198 199 <span class="i">$SequenceNum</span> = <span class="n">0</span><span class="sc">;</span> 200 <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span> 201 <span class="j">ID:</span> <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span> 202 <span class="i">$SequenceNum</span>++<span class="sc">;</span> 203 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="i">$SequenceNum</span>}<span class="s">)</span> <span class="s">{</span> 204 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> 205 <span class="s">}</span> 206 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceCount</span> >= <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="s">)</span> <span class="s">{</span> 207 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span> 208 <span class="s">}</span> 209 <span class="i">$SequenceCount</span>++<span class="sc">;</span> 210 211 <span class="c"># Collect sequence data...</span> 212 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> 213 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>->{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 214 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 215 <span class="s">}</span> 216 217 <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span> 218 <span class="s">}</span> 219 220 <span class="c"># Get specified sequence data...</span> <a name="GetDataBySequenceNumRange-"></a> 221 <span class="k">sub </span><span class="m">GetDataBySequenceNumRange</span> <span class="s">{</span> 222 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 223 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SequenceNum</span><span class="cm">,</span> <span class="i">$SequenceCount</span><span class="cm">,</span> <span class="i">%SpecifiedSequenceDataMap</span><span class="s">)</span><span class="sc">;</span> 224 225 <span class="c"># Go over sequences and collect sequences for writing out a new sequence file...</span> 226 <span class="i">%SpecifiedSequenceDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 227 <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 228 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 229 <span class="i">%</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 230 231 <span class="i">$SequenceNum</span> = <span class="n">0</span><span class="sc">;</span> 232 <span class="i">$SequenceCount</span> = <span class="n">0</span><span class="sc">;</span> 233 <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> 234 <span class="i">$SequenceNum</span>++<span class="sc">;</span> 235 236 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$SequenceNum</span> >= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">0</span>] && <span class="i">$SequenceNum</span> <= <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">1</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 237 <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span> 238 <span class="s">}</span> 239 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceNum</span> > <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span> 240 <span class="k">last</span> <span class="j">ID</span><span class="sc">;</span> 241 <span class="s">}</span> 242 <span class="i">$SequenceCount</span>++<span class="sc">;</span> 243 <span class="c"># Collect sequence data...</span> 244 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">IDs</span>}}<span class="cm">,</span> <span class="i">$ID</span><span class="sc">;</span> 245 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Description</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>->{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 246 <span class="i">$SpecifiedSequenceDataMap</span>{<span class="w">Sequence</span>}{<span class="i">$ID</span>} = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span> 247 <span class="s">}</span> 248 249 <span class="k">return</span> \<span class="i">%SpecifiedSequenceDataMap</span><span class="sc">;</span> 250 <span class="s">}</span> 251 252 253 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 254 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 255 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 256 257 <span class="c"># Miscellaneous options...</span> 258 <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> 259 260 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> 261 <span class="i">$OptionsInfo</span>{<span class="w">MatchExactSequenceIDs</span>} = <span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} =~ <span class="q">/Exact/i</span> ? <span class="n">1</span> <span class="co">:</span><span class="n">0</span><span class="sc">;</span> 262 263 <span class="c"># Check specified sequences value...</span> 264 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequences</span>} = <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span> 265 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 266 <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 267 268 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 269 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span> 270 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span> 271 <span class="k">die</span> <span class="q">"Error: No value specified for option \"-s, --Sequences\" during \"SequenceID\" of \"-m, --mode\" option\n"</span><span class="sc">;</span> 272 <span class="s">}</span> 273 <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span> 274 <span class="s">}</span> 275 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span> 276 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span> 277 <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span> 278 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="sc">;</span> 279 <span class="k">for</span> <span class="i">$SequenceNum</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span> 280 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 281 <span class="k">die</span> <span class="q">"Error: The value specified, $SequenceNum, in \"$Options{sequences}\" for option \"-s, --Sequences\" is not valid: Valid values: > 0\n"</span><span class="sc">;</span> 282 <span class="s">}</span> 283 <span class="s">}</span> 284 <span class="s">}</span> 285 <span class="k">else</span> <span class="s">{</span> 286 <span class="k">push</span> <span class="i">@SpecifiedSequenceIDs</span><span class="cm">,</span> <span class="q">"1"</span><span class="sc">;</span> 287 <span class="s">}</span> 288 <span class="s">}</span> 289 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span> 290 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">sequences</span>}<span class="s">)</span> <span class="s">{</span> 291 <span class="k">die</span> <span class="q">"Error: No value specified for option \"-s, --Sequences\" during \"SequenceNumRange\" of \"-m, --mode\" option\n"</span><span class="sc">;</span> 292 <span class="s">}</span> 293 <span class="i">@SpecifiedSequenceIDs</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">sequences</span>}<span class="sc">;</span> 294 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 295 <span class="k">die</span> <span class="q">"Error: The number of values"</span><span class="cm">,</span> <span class="k">scalar</span> <span class="i">@SpecifiedSequenceIDs</span><span class="cm">,</span> <span class="q">" specified, $Options{sequences}, for option \"-s, --Sequences\" are not valid. Number of values must be 2 to indicate starting and ending sequence number.\n"</span><span class="sc">;</span> 296 <span class="s">}</span> 297 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="sc">;</span> 298 <span class="k">for</span> <span class="i">$SequenceNum</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span> 299 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$SequenceNum</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 300 <span class="k">die</span> <span class="q">"Error: The value specified, $SequenceNum, in \"$Options{sequences}\" for option \"-s, --Sequences\" is not valid: Valid values: > 0\n"</span><span class="sc">;</span> 301 <span class="s">}</span> 302 <span class="s">}</span> 303 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedSequenceIDs</span>[<span class="n">0</span>] > <span class="i">$SpecifiedSequenceIDs</span>[<span class="n">1</span>]<span class="s">)</span> <span class="s">{</span> 304 <span class="k">die</span> <span class="q">"Error: The value specified \"$Options{sequences}\" for option \"-s, --Sequences\" are not valid: Starting sequence number $SpecifiedSequenceIDs[0] must be smaller than ending sequence number $SpecifiedSequenceIDs[1]\n"</span><span class="sc">;</span> 305 <span class="s">}</span> 306 <span class="s">}</span> 307 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDs</span>}}<span class="cm">,</span> <span class="i">@SpecifiedSequenceIDs</span><span class="sc">;</span> 308 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceID</span><span class="s">)</span><span class="sc">;</span> 309 <span class="k">for</span> <span class="i">$SequenceID</span> <span class="s">(</span><span class="i">@SpecifiedSequenceIDs</span><span class="s">)</span> <span class="s">{</span> 310 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span> 311 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="k">lc</span><span class="s">(</span><span class="i">$SequenceID</span><span class="s">)</span>} = <span class="i">$SequenceID</span><span class="sc">;</span> 312 <span class="s">}</span> 313 <span class="k">else</span> <span class="s">{</span> 314 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedSequenceIDsMap</span>}{<span class="i">$SequenceID</span>} = <span class="i">$SequenceID</span><span class="sc">;</span> 315 <span class="s">}</span> 316 <span class="s">}</span> 317 318 <span class="i">$OptionsInfo</span>{<span class="w">MaxSequenceLength</span>} = <span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="sc">;</span> 319 <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> 320 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 321 <span class="s">}</span> 322 323 <span class="c"># Retrieve information about sequence files...</span> <a name="RetrieveSequenceFilesInfo-"></a> 324 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span> 325 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FileDir</span><span class="cm">,</span> <span class="i">$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">$OutFileExt</span><span class="cm">,</span> <span class="i">$OutFileMode</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span> 326 327 <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 328 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 329 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 330 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 331 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 332 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 333 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 334 335 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span> 336 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 337 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 338 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 339 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 340 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 341 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="q">'NotSupported'</span><span class="sc">;</span> 342 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 343 344 <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> 345 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 346 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 347 <span class="s">}</span> 348 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span> 349 350 <span class="s">(</span><span class="i">$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> 351 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span> 352 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n"</span><span class="sc">;</span> 353 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 354 <span class="s">}</span> 355 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span> 356 357 <span class="i">$SequenceCount</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span> 358 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SequenceCount</span><span class="s">)</span> <span class="s">{</span> 359 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence data is missing.\n"</span><span class="sc">;</span> 360 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 361 <span class="s">}</span> 362 363 <span class="c"># Setup output file names...</span> 364 <span class="i">$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> 365 <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> 366 <span class="i">$OutFileExt</span> = <span class="q">'fasta'</span><span class="sc">;</span> 367 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 368 <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> 369 <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> 370 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> 371 <span class="s">}</span> 372 <span class="k">else</span> <span class="s">{</span> 373 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> 374 <span class="s">}</span> 375 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> 376 <span class="s">}</span> 377 <span class="k">else</span> <span class="s">{</span> 378 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> 379 <span class="s">}</span> 380 <span class="j">MODE:</span> <span class="s">{</span> 381 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceID$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'SequenceID'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> 382 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceNum$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'SequenceNum'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> 383 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^SequenceNumRange$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$OutFileMode</span> = <span class="q">'SequenceNumRange'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span> 384 <span class="i">$OutFileMode</span> = <span class="q">''</span><span class="sc">;</span> 385 <span class="s">}</span> 386 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> 387 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}${OutFileMode}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> 388 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}${OutFileMode}.${OutFileExt} already exists\n"</span><span class="sc">;</span> 389 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 390 <span class="s">}</span> 391 <span class="s">}</span> 392 393 <span class="i">$SequenceFilesInfo</span>{<span class="w">FilesOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> 394 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> 395 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span> 396 <span class="i">$SequenceFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">"${OutFileRoot}${OutFileMode}.${OutFileExt}"</span><span class="sc">;</span> 397 398 <span class="i">$SequenceFilesInfo</span>{<span class="w">Format</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span> 399 <span class="i">$SequenceFilesInfo</span>{<span class="w">SequenceCount</span>}[<span class="i">$Index</span>] = <span class="i">$SequenceCount</span><span class="sc">;</span> 400 <span class="s">}</span> 401 <span class="s">}</span> 402 403 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 404 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 405 406 <span class="c"># Retrieve all the options...</span> 407 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 408 <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">'Yes'</span><span class="sc">;</span> 409 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'SequenceNum'</span><span class="sc">;</span> 410 <span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} = <span class="q">'Relaxed'</span><span class="sc">;</span> 411 <span class="i">$Options</span>{<span class="w">sequencelength</span>} = <span class="n">80</span><span class="sc">;</span> 412 413 <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">"overwrite|o"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"sequences|s=s"</span><span class="cm">,</span> <span class="q">"sequenceidmatch=s"</span><span class="cm">,</span> <span class="q">"sequencelength=i"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 414 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 415 <span class="s">}</span> 416 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 417 <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> 418 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 419 <span class="s">}</span> 420 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> 421 <span class="s">}</span> 422 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> 423 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ignoregaps}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> 424 <span class="s">}</span> 425 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(SequenceID|SequenceNum|SequenceNumRange)$/i</span><span class="s">)</span> <span class="s">{</span> 426 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: SequenceID, SequenceNum, or SequenceNumRange\n"</span><span class="sc">;</span> 427 <span class="s">}</span> 428 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">sequenceidmatch</span>} !~ <span class="q">/^(Exact|Relaxed)$/i</span><span class="s">)</span> <span class="s">{</span> 429 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequenceidmatch}, for option \"--SequenceIDMatch\" is not valid. Allowed values: Exact or Relaxed\n"</span><span class="sc">;</span> 430 <span class="s">}</span> 431 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">sequencelength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 432 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{sequencelength}, for option \"--SequenceLength\" is not valid. Allowed values: >0\n"</span><span class="sc">;</span> 433 <span class="s">}</span> 434 <span class="s">}</span> 435 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>