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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:InfoSequenceFiles.pl</title>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: InfoSequenceFiles.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
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18 5 <span class="c"># $Revision: 1.29 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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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>
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44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">SequenceFileUtil</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">StatisticsUtil</span><span class="sc">;</span>
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52 39
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53 40 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
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54 41
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55 42 <span class="c"># Autoflush STDOUT</span>
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56 43 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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57 44
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58 45 <span class="c"># Starting message...</span>
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59 46 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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60 47 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
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61 48 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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62 49
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63 50 <span class="c"># Get the options and setup script...</span>
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64 51 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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65 52 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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66 53 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span>
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67 54 <span class="s">}</span>
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68 55
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69 56 <span class="k">my</span><span class="s">(</span><span class="i">@SequenceFilesList</span><span class="s">)</span><span class="sc">;</span>
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70 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>
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71 58
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72 59 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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73 60 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
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74 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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75 62
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76 63 <span class="k">print</span> <span class="q">"Checking input sequence file(s)...\n"</span><span class="sc">;</span>
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77 64 <span class="k">my</span><span class="s">(</span><span class="i">%SequenceFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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78 65 <span class="i">RetrieveSequenceFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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79 66
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80 67 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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81 68 <span class="k">if</span> <span class="s">(</span><span class="i">@SequenceFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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82 69 <span class="k">print</span> <span class="q">"\nProcessing sequence files...\n"</span><span class="sc">;</span>
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83 70 <span class="s">}</span>
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84 71 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
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85 72 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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86 73 <span class="k">print</span> <span class="q">"\nProcessing file $SequenceFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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87 74 <span class="i">ListSequenceFileInfo</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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88 75 <span class="s">}</span>
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89 76 <span class="s">}</span>
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90 77 <span class="i">ListTotalSizeOfFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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91 78
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92 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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93 80
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94 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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95 82 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span>
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96 83 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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97 84
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98 85 <span class="c">###############################################################################</span>
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99 86
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100 87 <span class="c"># List appropriate information...</span>
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101 <a name="ListSequenceFileInfo-"></a> 88 <span class="k">sub </span><span class="m">ListSequenceFileInfo</span> <span class="s">{</span>
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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103 90 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
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104 91
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105 92 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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106 93
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107 94 <span class="i">$SequenceDataRef</span> = <span class="i">ReadSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
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108 95
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109 96 <span class="k">my</span><span class="s">(</span><span class="i">$SequencesCount</span><span class="s">)</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Count</span>}<span class="sc">;</span>
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110 97 <span class="k">print</span> <span class="q">"\nNumber of sequences: $SequencesCount\n"</span><span class="sc">;</span>
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111 98
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112 99 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListShortestSequence</span>} && <span class="s">(</span><span class="i">$SequencesCount</span> > <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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113 100 <span class="k">my</span><span class="s">(</span><span class="i">$ShortestSeqID</span><span class="cm">,</span> <span class="i">$ShortestSeq</span><span class="cm">,</span> <span class="i">$ShortestSeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="i">GetShortestSequence</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
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114 101 <span class="k">print</span> <span class="q">"\nShortest sequence information:\nID: $ShortestSeqID; Length:$ShortestSeqLen\n"</span><span class="sc">;</span>
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115 102 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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116 103 <span class="k">print</span> <span class="q">"Description: $Description\n"</span><span class="sc">;</span>
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117 104 <span class="s">}</span>
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118 105 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
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119 106 <span class="k">print</span> <span class="q">"Sequence: $ShortestSeq\n"</span><span class="sc">;</span>
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120 107 <span class="s">}</span>
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121 108 <span class="s">}</span>
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122 109 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListLongestSequence</span>} && <span class="s">(</span><span class="i">$SequencesCount</span> > <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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123 110 <span class="k">my</span><span class="s">(</span><span class="i">$LongestSeqID</span><span class="cm">,</span> <span class="i">$LongestSeq</span><span class="cm">,</span> <span class="i">$LongestSeqLen</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span> = <span class="i">GetLongestSequence</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
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124 111 <span class="k">print</span> <span class="q">"\nLongest sequence information:\nID: $LongestSeqID; Length: $LongestSeqLen\n"</span><span class="sc">;</span>
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125 112 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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126 113 <span class="k">print</span> <span class="q">"Description: $Description\n"</span><span class="sc">;</span>
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127 114 <span class="s">}</span>
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128 115 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
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129 116 <span class="k">print</span> <span class="q">"Sequence: $LongestSeq\n"</span><span class="sc">;</span>
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130 117 <span class="s">}</span>
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131 118 <span class="s">}</span>
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132 119 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FrequencyAnalysis</span>} && <span class="s">(</span><span class="i">$SequencesCount</span> > <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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133 120 <span class="i">PerformLengthFrequencyAnalysis</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ListSequenceLengths</span>}<span class="s">)</span> <span class="s">{</span>
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136 123 <span class="i">ListSequenceLengths</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span><span class="sc">;</span>
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137 124 <span class="s">}</span>
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138 125
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139 126 <span class="c"># File size and modification information...</span>
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140 127 <span class="k">print</span> <span class="q">"\nFile size: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span>
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141 128 <span class="k">print</span> <span class="q">"Last modified: "</span><span class="cm">,</span> <span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">" \n"</span><span class="sc">;</span>
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142 129 <span class="s">}</span>
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143 130
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144 131 <span class="c"># List information about sequence lengths...</span>
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145 <a name="ListSequenceLengths-"></a> 132 <span class="k">sub </span><span class="m">ListSequenceLengths</span> <span class="s">{</span>
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146 133 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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147 134 <span class="k">my</span><span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$Description</span><span class="s">)</span><span class="sc">;</span>
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148 135
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149 136 <span class="k">print</span> <span class="q">"\nSequence lengths information:\n"</span><span class="sc">;</span>
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150 137 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
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151 138 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
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152 139 <span class="i">$Description</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Description</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
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153 140 <span class="i">$SeqLen</span> = <span class="i">GetSequenceLength</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
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154 141 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span> <span class="s">{</span>
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155 142 <span class="i">$Sequence</span> = <span class="i">RemoveSequenceGaps</span><span class="s">(</span><span class="i">$Sequence</span><span class="s">)</span><span class="sc">;</span>
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156 143 <span class="s">}</span>
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157 144 <span class="k">print</span> <span class="q">"ID: $ID; Length:$SeqLen\n"</span><span class="sc">;</span>
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158 145 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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159 146 <span class="k">print</span> <span class="q">"Description: $Description\n"</span><span class="sc">;</span>
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160 147 <span class="s">}</span>
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161 148 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
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162 149 <span class="k">print</span> <span class="q">"Sequence: $Sequence\n"</span><span class="sc">;</span>
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163 150 <span class="s">}</span>
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164 151 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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165 152 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
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166 153 <span class="s">}</span>
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167 154 <span class="s">}</span>
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168 155 <span class="s">}</span>
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169 156
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170 157 <span class="c"># Total size of all the fiels...</span>
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171 <a name="ListTotalSizeOfFiles-"></a> 158 <span class="k">sub </span><span class="m">ListTotalSizeOfFiles</span> <span class="s">{</span>
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172 159 <span class="k">my</span><span class="s">(</span><span class="i">$FileOkayCount</span><span class="cm">,</span> <span class="i">$TotalSize</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
|
|
|
173 160
|
|
|
174 161 <span class="i">$FileOkayCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
175 162 <span class="i">$TotalSize</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
176 163
|
|
|
177 164 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
178 165 <span class="k">if</span> <span class="s">(</span><span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
179 166 <span class="i">$FileOkayCount</span>++<span class="sc">;</span>
|
|
|
180 167 <span class="i">$TotalSize</span> += <span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
181 168 <span class="s">}</span>
|
|
|
182 169 <span class="s">}</span>
|
|
|
183 170 <span class="k">if</span> <span class="s">(</span><span class="i">$FileOkayCount</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
184 171 <span class="k">print</span> <span class="q">"\nTotal size of $FileOkayCount files: "</span><span class="cm">,</span> <span class="i">FormatFileSize</span><span class="s">(</span><span class="i">$TotalSize</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
185 172 <span class="s">}</span>
|
|
|
186 173 <span class="s">}</span>
|
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|
187 174
|
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|
188 175
|
|
|
189 176 <span class="c"># Perform frequency analysis of sequence lengths</span>
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|
190 <a name="PerformLengthFrequencyAnalysis-"></a> 177 <span class="k">sub </span><span class="m">PerformLengthFrequencyAnalysis</span> <span class="s">{</span>
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|
|
191 178 <span class="k">my</span><span class="s">(</span><span class="i">$SequenceDataRef</span><span class="cm">,</span> <span class="i">$SequenceLengthsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
192 179 <span class="k">my</span> <span class="s">(</span><span class="i">$ID</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="cm">,</span> <span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$SequenceLenBin</span><span class="cm">,</span> <span class="i">$LenBin</span><span class="cm">,</span> <span class="i">$SequenceLenCount</span><span class="cm">,</span> <span class="i">@SequenceLengths</span><span class="cm">,</span> <span class="i">%SequenceLenFrequency</span><span class="s">)</span><span class="sc">;</span>
|
|
|
193 180
|
|
|
194 181 <span class="i">@SequenceLengths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
195 182 <span class="i">%SequenceLenFrequency</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
196 183 <span class="k">for</span> <span class="i">$ID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$SequenceDataRef</span>->{<span class="w">IDs</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
197 184 <span class="i">$Sequence</span> = <span class="i">$SequenceDataRef</span>->{<span class="w">Sequence</span>}{<span class="i">$ID</span>}<span class="sc">;</span>
|
|
|
198 185 <span class="i">$SeqLen</span> = <span class="i">GetSequenceLength</span><span class="s">(</span><span class="i">$Sequence</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
199 186 <span class="k">push</span> <span class="i">@SequenceLengths</span><span class="cm">,</span> <span class="i">$SeqLen</span><span class="sc">;</span>
|
|
|
200 187 <span class="s">}</span>
|
|
|
201 188 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
202 189 <span class="i">%SequenceLenFrequency</span> = <span class="i">Frequency</span><span class="s">(</span>\<span class="i">@SequenceLengths</span><span class="cm">,</span> \<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
203 190 <span class="s">}</span>
|
|
|
204 191 <span class="k">else</span> <span class="s">{</span>
|
|
|
205 192 <span class="i">%SequenceLenFrequency</span> = <span class="i">Frequency</span><span class="s">(</span>\<span class="i">@SequenceLengths</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
206 193 <span class="s">}</span>
|
|
|
207 194 <span class="k">print</span> <span class="q">"\nDistribution of sequence lengths (LengthBin => Count):\n"</span><span class="sc">;</span>
|
|
|
208 195 <span class="k">for</span> <span class="i">$SequenceLenBin</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%SequenceLenFrequency</span><span class="s">)</span> <span class="s">{</span>
|
|
|
209 196 <span class="i">$SequenceLenCount</span> = <span class="i">$SequenceLenFrequency</span>{<span class="i">$SequenceLenBin</span>}<span class="sc">;</span>
|
|
|
210 197 <span class="i">$LenBin</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">"%.1f"</span><span class="cm">,</span> <span class="i">$SequenceLenBin</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
211 198 <span class="k">print</span> <span class="q">"$LenBin => $SequenceLenCount; "</span><span class="sc">;</span>
|
|
|
212 199 <span class="s">}</span>
|
|
|
213 200 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
214 201 <span class="s">}</span>
|
|
|
215 202
|
|
|
216 203 <span class="c"># Retrieve information about sequence files...</span>
|
|
|
217 <a name="RetrieveSequenceFilesInfo-"></a> 204 <span class="k">sub </span><span class="m">RetrieveSequenceFilesInfo</span> <span class="s">{</span>
|
|
|
218 205 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SequenceFile</span><span class="cm">,</span> <span class="i">$FileSupported</span><span class="cm">,</span> <span class="i">$FileFormat</span><span class="cm">,</span> <span class="i">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
219 206
|
|
|
220 207 <span class="i">%SequenceFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
221 208 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
222 209 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileFormat</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
223 210 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
224 211 <span class="i">@</span>{<span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
225 212
|
|
|
226 213 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SequenceFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
227 214 <span class="i">$SequenceFile</span> = <span class="i">$SequenceFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
228 215
|
|
|
229 216 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">SEQUENCEFILE</span><span class="cm">,</span> <span class="q">"$SequenceFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
230 217 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
|
|
|
231 218 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
232 219 <span class="s">}</span>
|
|
|
233 220 <span class="k">close</span> <span class="w">SEQUENCEFILE</span><span class="sc">;</span>
|
|
|
234 221
|
|
|
235 222 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
236 223 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileFormat</span>}[<span class="i">$Index</span>] = <span class="q">'NotSupported'</span><span class="sc">;</span>
|
|
|
237 224 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
238 225 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
|
|
|
239 226
|
|
|
240 227 <span class="s">(</span><span class="i">$FileSupported</span><span class="cm">,</span> <span class="i">$FileFormat</span><span class="s">)</span> = <span class="i">IsSupportedSequenceFile</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
241 228 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FileSupported</span><span class="s">)</span> <span class="s">{</span>
|
|
|
242 229 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n"</span><span class="sc">;</span>
|
|
|
243 230 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
244 231 <span class="s">}</span>
|
|
|
245 232
|
|
|
246 233 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
247 234 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileFormat</span>}[<span class="i">$Index</span>] = <span class="i">$FileFormat</span><span class="sc">;</span>
|
|
|
248 235 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileSize</span>}[<span class="i">$Index</span>] = <span class="i">FileSize</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
249 236
|
|
|
250 237 <span class="s">(</span><span class="i">$ModifiedTimeString</span><span class="cm">,</span> <span class="i">$ModifiedDateString</span><span class="s">)</span> = <span class="i">FormattedFileModificationTimeAndDate</span><span class="s">(</span><span class="i">$SequenceFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
251 238 <span class="i">$SequenceFilesInfo</span>{<span class="w">FileLastModified</span>}[<span class="i">$Index</span>] = <span class="q">"$ModifiedTimeString; $ModifiedDateString"</span><span class="sc">;</span>
|
|
|
252 239 <span class="s">}</span>
|
|
|
253 240 <span class="s">}</span>
|
|
|
254 241
|
|
|
255 242 <span class="c"># Process option values...</span>
|
|
|
256 <a name="ProcessOptions-"></a> 243 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
257 244
|
|
|
258 245 <span class="i">$OptionsInfo</span>{<span class="w">All</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">all</span>} ? <span class="i">$Options</span>{<span class="w">all</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
259 246
|
|
|
260 247 <span class="i">$OptionsInfo</span>{<span class="w">Count</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">count</span>} ? <span class="i">$Options</span>{<span class="w">count</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
261 248 <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
|
|
|
262 249 <span class="i">$OptionsInfo</span>{<span class="w">Frequency</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">frequency</span>} ? <span class="i">$Options</span>{<span class="w">frequency</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
263 250 <span class="i">$OptionsInfo</span>{<span class="w">FrequencyBins</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">frequencybins</span>} ? <span class="i">$Options</span>{<span class="w">frequencybins</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
264 251 <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">ignoregaps</span>} ? <span class="i">$Options</span>{<span class="w">ignoregaps</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
265 252 <span class="i">$OptionsInfo</span>{<span class="w">Longest</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">longest</span>} ? <span class="i">$Options</span>{<span class="w">longest</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
266 253 <span class="i">$OptionsInfo</span>{<span class="w">Shortest</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">shortest</span>} ? <span class="i">$Options</span>{<span class="w">shortest</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
267 254 <span class="i">$OptionsInfo</span>{<span class="w">SequenceLengths</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">sequencelengths</span>} ? <span class="i">$Options</span>{<span class="w">sequencelengths</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
268 255
|
|
|
269 256 <span class="i">$OptionsInfo</span>{<span class="w">FrequencyAnalysis</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">frequency</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
270 257 <span class="i">$OptionsInfo</span>{<span class="w">ListLongestSequence</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">longest</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
271 258 <span class="i">$OptionsInfo</span>{<span class="w">ListShortestSequence</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">shortest</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
272 259 <span class="i">$OptionsInfo</span>{<span class="w">ListSequenceLengths</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">all</span>} || <span class="i">$Options</span>{<span class="w">sequencelengths</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
273 260 <span class="i">$OptionsInfo</span>{<span class="w">IgnoreGaps</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} =~ <span class="q">/Yes/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
274 261
|
|
|
275 262 <span class="c"># Setup frequency bin values...</span>
|
|
|
276 263 <span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>} = <span class="n">4</span><span class="sc">;</span>
|
|
|
277 264 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
278 265
|
|
|
279 266 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">frequencybins</span>} =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
280 267 <span class="k">my</span><span class="s">(</span><span class="i">$BinValue</span><span class="cm">,</span> <span class="i">@SpecifiedBinRange</span><span class="s">)</span><span class="sc">;</span>
|
|
|
281 268 <span class="i">@SpecifiedBinRange</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">frequencybins</span>}<span class="sc">;</span>
|
|
|
282 269 <span class="k">if</span> <span class="s">(</span><span class="i">@SpecifiedBinRange</span> < <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
283 270 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain at least two values. \n"</span><span class="sc">;</span>
|
|
|
284 271 <span class="s">}</span>
|
|
|
285 272 <span class="k">for</span> <span class="i">$BinValue</span> <span class="s">(</span><span class="i">@SpecifiedBinRange</span><span class="s">)</span> <span class="s">{</span>
|
|
|
286 273 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsNumerical</span><span class="s">(</span><span class="i">$BinValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
287 274 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Contains non numeric values. \n"</span><span class="sc">;</span>
|
|
|
288 275 <span class="s">}</span>
|
|
|
289 276 <span class="s">}</span>
|
|
|
290 277 <span class="k">my</span><span class="s">(</span><span class="i">$Index1</span><span class="cm">,</span> <span class="i">$Index2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
291 278 <span class="k">for</span> <span class="i">$Index1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SpecifiedBinRange</span><span class="s">)</span> <span class="s">{</span>
|
|
|
292 279 <span class="k">for</span> <span class="i">$Index2</span> <span class="s">(</span><span class="s">(</span><span class="i">$Index1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#SpecifiedBinRange</span><span class="s">)</span> <span class="s">{</span>
|
|
|
293 280 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedBinRange</span>[<span class="i">$Index1</span>] >= <span class="i">$SpecifiedBinRange</span>[<span class="i">$Index2</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
294 281 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain values in ascending order. \n"</span><span class="sc">;</span>
|
|
|
295 282 <span class="s">}</span>
|
|
|
296 283 <span class="s">}</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">BinRange</span>}}<span class="cm">,</span> <span class="i">@SpecifiedBinRange</span><span class="sc">;</span>
|
|
|
299 286 <span class="s">}</span>
|
|
|
300 287 <span class="k">else</span> <span class="s">{</span>
|
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301 288 <span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>} = <span class="i">$Options</span>{<span class="w">frequencybins</span>}<span class="sc">;</span>
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302 289 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">NumOfBins</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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303 290 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid. Allowed values: positive integer or \"number,number,[number]...\". \n"</span><span class="sc">;</span>
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304 291 <span class="s">}</span>
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305 292 <span class="s">}</span>
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306 293 <span class="s">}</span>
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307 294
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308 295 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
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309 <a name="SetupScriptUsage-"></a> 296 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
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310 297
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311 298 <span class="c"># Retrieve all the options...</span>
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312 299 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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313 300 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
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314 301 <span class="i">$Options</span>{<span class="w">ignoregaps</span>} = <span class="q">'no'</span><span class="sc">;</span>
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315 302 <span class="i">$Options</span>{<span class="w">frequencybins</span>} = <span class="n">10</span><span class="sc">;</span>
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316 303
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317 304 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"all|a"</span><span class="cm">,</span> <span class="q">"count|c"</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"frequency|f"</span><span class="cm">,</span> <span class="q">"frequencybins=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"ignoregaps|i=s"</span><span class="cm">,</span> <span class="q">"longest|l"</span><span class="cm">,</span> <span class="q">"shortest|s"</span><span class="cm">,</span> <span class="q">"sequencelengths"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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318 305 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
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319 306 <span class="s">}</span>
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320 307 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
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321 308 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
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322 309 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
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323 310 <span class="s">}</span>
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324 311 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span>
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325 312 <span class="s">}</span>
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326 313 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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327 314 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n"</span><span class="sc">;</span>
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328 315 <span class="s">}</span>
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329 316 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignoregaps</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
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330 317 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ignoregaps}, for option \"-i --IgnoreGaps\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
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331 318 <span class="s">}</span>
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332 319 <span class="s">}</span>
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333 320
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334 <a name="EOF-"></a></pre>
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335 <p> </p>
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336 <br />
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337 <center>
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338 <img src="../../../images/h2o2.png">
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339 </center>
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340 </body>
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341 </html>
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