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1 <html>
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3 <title>MayaChemTools:Code:JoinTextFiles.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: JoinTextFiles.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: 1.32 $</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
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51 38 <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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52 39
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53 40 <span class="c"># Autoflush STDOUT</span>
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54 41 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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55 42
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56 43 <span class="c"># Starting message...</span>
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57 44 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span>
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58 45 <span class="k">print</span> <span class="q">"\n$ScriptName:Starting...\n\n"</span><span class="sc">;</span>
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59 46 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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60 47
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61 48 <span class="c"># Get the options and setup script...</span>
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62 49 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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63 50 <span class="k">if</span> <span class="s">(</span><span class="i">$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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64 51 <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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65 52 <span class="s">}</span>
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66 53
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67 54 <span class="k">my</span><span class="s">(</span><span class="i">@TextFilesList</span><span class="s">)</span><span class="sc">;</span>
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68 55 <span class="i">@TextFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="sc">;</span>
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69 56
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70 57 <span class="k">if</span> <span class="s">(</span><span class="i">@TextFilesList</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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71 58 <span class="k">die</span> <span class="q">"Error: Specify more than one Text file.\n"</span><span class="sc">;</span>
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72 59 <span class="s">}</span>
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73 60
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74 61 <span class="c"># Process options...</span>
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75 62 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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76 63 <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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77 64 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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78 65
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79 66 <span class="c"># Setup information about input files...</span>
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80 67 <span class="k">print</span> <span class="q">"Checking input text files...\n"</span><span class="sc">;</span>
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81 68 <span class="k">my</span><span class="s">(</span><span class="i">%TextFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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82 69 <span class="i">RetrieveTextFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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83 70
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84 71 <span class="c"># Join files...</span>
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85 72 <span class="k">print</span> <span class="q">"\nGenerating new text file $OptionsInfo{NewTextFile}...\n"</span><span class="sc">;</span>
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86 73 <span class="i">JoinTextFiles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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87 74
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88 75 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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89 76
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90 77 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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91 78 <span class="i">$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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92 79 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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93 80
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94 81 <span class="c">###############################################################################</span>
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95 82
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96 83 <span class="c"># Join all valid Text files...</span>
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97 <a name="JoinTextFiles-"></a> 84 <span class="k">sub </span><span class="m">JoinTextFiles</span> <span class="s">{</span>
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98 85 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$FirstColLabelsLine</span><span class="cm">,</span> <span class="i">$OutDelim</span><span class="cm">,</span> <span class="i">$OutQuote</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">@Words</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
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99 86
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100 87 <span class="i">$NewTextFile</span> = <span class="i">$OptionsInfo</span>{<span class="w">NewTextFile</span>}<span class="sc">;</span>
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101 88
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102 89 <span class="i">$FirstColLabelsLine</span> = <span class="q">''</span><span class="sc">;</span>
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103 90
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104 91 <span class="i">$OutDelim</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="sc">;</span> <span class="i">$OutQuote</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="sc">;</span>
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105 92
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106 93 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewTextFile: $! \n"</span><span class="sc">;</span>
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107 94 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span>
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108 95 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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109 96 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
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110 97 <span class="s">}</span>
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111 98
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112 99 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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113 100 <span class="i">$InDelim</span> = <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
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114 101
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115 102 <span class="k">print</span> <span class="q">"\nProcessing file $TextFile...\n"</span><span class="sc">;</span>
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116 103
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117 104 <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $TextFile: $! \n"</span><span class="sc">;</span>
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118 105
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119 106 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Label</span>}<span class="s">)</span> <span class="s">{</span>
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120 107 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Fast</span>}<span class="s">)</span> <span class="s">{</span>
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121 108 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
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122 109 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FirstColLabelsLine</span><span class="s">)</span> <span class="s">{</span>
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123 110 <span class="i">$FirstColLabelsLine</span> = <span class="i">$Line</span><span class="sc">;</span>
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124 111 <span class="k">print</span> <span class="i">NEWTEXTFILE</span> <span class="q">"$FirstColLabelsLine\n"</span><span class="sc">;</span>
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125 112 <span class="s">}</span>
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126 113 <span class="s">}</span>
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127 114 <span class="k">else</span> <span class="s">{</span>
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128 115 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
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129 116 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FirstColLabelsLine</span><span class="s">)</span> <span class="s">{</span>
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130 117 <span class="i">@ColLabels</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
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131 118 <span class="i">$FirstColLabelsLine</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OutDelim</span><span class="cm">,</span> <span class="i">$OutQuote</span><span class="s">)</span><span class="sc">;</span>
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132 119 <span class="k">print</span> <span class="i">NEWTEXTFILE</span> <span class="q">"$FirstColLabelsLine\n"</span><span class="sc">;</span>
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133 120 <span class="s">}</span>
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134 121 <span class="s">}</span>
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135 122 <span class="s">}</span>
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136 123
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137 124 <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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138 125 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">Fast</span>}<span class="s">)</span> <span class="s">{</span>
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139 126 <span class="i">@Words</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
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140 127 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@Words</span><span class="cm">,</span> <span class="i">$OutDelim</span><span class="cm">,</span> <span class="i">$OutQuote</span><span class="s">)</span><span class="sc">;</span>
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141 128 <span class="s">}</span>
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142 129 <span class="k">print</span> <span class="i">NEWTEXTFILE</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
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143 130 <span class="s">}</span>
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144 131 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span>
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145 132 <span class="s">}</span>
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146 133
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147 134 <span class="k">close</span> <span class="w">NEWTEXTFILE</span><span class="sc">;</span>
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148 135 <span class="s">}</span>
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149 136
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150 137 <span class="c"># Retrieve information about Text files...</span>
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151 <a name="RetrieveTextFilesInfo-"></a> 138 <span class="k">sub </span><span class="m">RetrieveTextFilesInfo</span> <span class="s">{</span>
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152 139 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$FirstColLabelsLine</span><span class="cm">,</span> <span class="i">$ColLabelsLine</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">$FileExt</span><span class="cm">,</span> <span class="i">@FirstColLabels</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
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153 140
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154 141 <span class="i">%TextFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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155 142 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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156 143 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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157 144
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158 145 <span class="i">$FirstColLabelsLine</span> = <span class="q">''</span><span class="sc">;</span> <span class="i">$ColLabelsLine</span> = <span class="q">''</span><span class="sc">;</span>
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159 146 <span class="i">@FirstColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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160 147
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161 148 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span>
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162 149 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
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163 150 <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span>
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164 151
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165 152 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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166 153 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$TextFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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167 154 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: It doesn't exist\n"</span><span class="sc">;</span>
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168 155 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
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169 156 <span class="s">}</span>
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170 157 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$TextFile</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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171 158 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: It's not a Text file\n"</span><span class="sc">;</span>
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172 159 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
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173 160 <span class="s">}</span>
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174 161
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175 162 <span class="s">(</span><span class="i">$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">$TextFile</span><span class="s">)</span><span class="sc">;</span>
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176 163 <span class="k">if</span> <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
177 164 <span class="i">$InDelim</span> = <span class="q">"\t"</span><span class="sc">;</span>
|
|
|
178 165 <span class="s">}</span>
|
|
|
179 166 <span class="k">else</span> <span class="s">{</span>
|
|
|
180 167 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span>
|
|
|
181 168 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
182 169 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: The value specified, $OptionsInfo{InDelim}, for option \"--indelim\" is not valid for csv files\n"</span><span class="sc">;</span>
|
|
|
183 170 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
184 171 <span class="s">}</span>
|
|
|
185 172 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
186 173 <span class="i">$InDelim</span> = <span class="q">"\;"</span><span class="sc">;</span>
|
|
|
187 174 <span class="s">}</span>
|
|
|
188 175 <span class="s">}</span>
|
|
|
189 176
|
|
|
190 177 <span class="k">if</span> <span class="s">(</span>! <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
191 178 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
|
|
|
192 179 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
193 180 <span class="s">}</span>
|
|
|
194 181 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
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|
195 182 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span>
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196 183
|
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|
197 184 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Label</span>}<span class="s">)</span> <span class="s">{</span>
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|
198 185 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">Fast</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
199 186 <span class="i">@ColLabels</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
200 187 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstColLabelsLine</span><span class="s">)</span> <span class="s">{</span>
|
|
|
201 188 <span class="k">if</span> <span class="s">(</span><span class="i">@ColLabels</span> != <span class="i">@FirstColLabels</span><span class="s">)</span> <span class="s">{</span>
|
|
|
202 189 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: The number of columns in this file, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@ColLabels</span><span class="s">)</span><span class="cm">,</span> <span class="q">", is different from the number of columns, "</span><span class="cm">,</span> <span class="k">scalar</span><span class="s">(</span><span class="i">@FirstColLabels</span><span class="s">)</span><span class="cm">,</span> <span class="q">", in the first valid text file. \n"</span><span class="sc">;</span>
|
|
|
203 190 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
204 191 <span class="s">}</span>
|
|
|
205 192 <span class="i">$ColLabelsLine</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
206 193 <span class="k">if</span> <span class="s">(</span><span class="i">$ColLabelsLine</span> <span class="k">ne</span> <span class="i">$FirstColLabelsLine</span><span class="s">)</span> <span class="s">{</span>
|
|
|
207 194 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: The column names in this file are different from those in first valid text file.\nColumnlabels in first valid text file: $FirstColLabelsLine \nColumnlabels in current text file: $ColLabelsLine\n"</span><span class="sc">;</span>
|
|
|
208 195 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
209 196 <span class="s">}</span>
|
|
|
210 197 <span class="s">}</span>
|
|
|
211 198 <span class="k">else</span> <span class="s">{</span>
|
|
|
212 199 <span class="i">@FirstColLabels</span> = <span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
213 200 <span class="i">$FirstColLabelsLine</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@FirstColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
214 201 <span class="s">}</span>
|
|
|
215 202 <span class="s">}</span>
|
|
|
216 203 <span class="s">}</span>
|
|
|
217 204
|
|
|
218 205 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
219 206 <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="i">$InDelim</span><span class="sc">;</span>
|
|
|
220 207 <span class="s">}</span>
|
|
|
221 208 <span class="s">}</span>
|
|
|
222 209
|
|
|
223 210 <span class="c"># Process option values...</span>
|
|
|
224 <a name="ProcessOptions-"></a> 211 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
225 212 <span class="k">my</span><span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
|
|
|
226 213
|
|
|
227 214 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
228 215
|
|
|
229 216 <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="i">$Options</span>{<span class="w">fast</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
230 217
|
|
|
231 218 <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} = <span class="i">$Options</span>{<span class="w">indelim</span>}<span class="sc">;</span>
|
|
|
232 219 <span class="i">$OptionsInfo</span>{<span class="w">Label</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">label</span>} =~ <span class="q">/^yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
233 220
|
|
|
234 221 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
235 222 <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
236 223
|
|
|
237 224 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
238 225 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
239 226
|
|
|
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
241 228 <span class="i">$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>
|
|
|
242 229 <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">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
243 230 <span class="k">if</span> <span class="s">(</span><span class="i">$FileName</span> && <span class="i">$FileExt</span><span class="s">)</span> <span class="s">{</span>
|
|
|
244 231 <span class="i">$NewTextFile</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
245 232 <span class="s">}</span>
|
|
|
246 233 <span class="k">else</span> <span class="s">{</span>
|
|
|
247 234 <span class="i">$NewTextFile</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
|
|
|
248 235 <span class="s">}</span>
|
|
|
249 236 <span class="s">}</span>
|
|
|
250 237 <span class="k">else</span> <span class="s">{</span>
|
|
|
251 238 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
252 239 <span class="s">(</span><span class="i">$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">$TextFilesList</span>[<span class="n">0</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
253 240 <span class="i">$NewTextFile</span> = <span class="i">$FileName</span> . <span class="q">"1To"</span> . <span class="i">@TextFilesList</span> . <span class="q">"Joined"</span><span class="sc">;</span>
|
|
|
254 241 <span class="s">}</span>
|
|
|
255 242
|
|
|
256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
257 244 <span class="i">$NewTextFile</span> .= <span class="q">".tsv"</span><span class="sc">;</span>
|
|
|
258 245 <span class="s">}</span>
|
|
|
259 246 <span class="k">else</span> <span class="s">{</span>
|
|
|
260 247 <span class="i">$NewTextFile</span> .= <span class="q">".csv"</span><span class="sc">;</span>
|
|
|
261 248 <span class="s">}</span>
|
|
|
262 249
|
|
|
263 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
264 251 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewTextFile</span><span class="s">)</span> <span class="s">{</span>
|
|
|
265 252 <span class="k">die</span> <span class="q">"Error: The file $NewTextFile already exists.\n"</span><span class="sc">;</span>
|
|
|
266 253 <span class="s">}</span>
|
|
|
267 254 <span class="s">}</span>
|
|
|
268 255
|
|
|
269 256 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
270 257 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span>
|
|
|
271 258 <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$NewTextFile</span><span class="s">)</span> <span class="k">eq</span> <span class="k">lc</span><span class="s">(</span><span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
272 259 <span class="k">die</span> <span class="q">"Error: Output filename, $NewTextFile, is similar to a input file name.\nSpecify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
|
|
|
273 260 <span class="s">}</span>
|
|
|
274 261 <span class="s">}</span>
|
|
|
275 262 <span class="s">}</span>
|
|
|
276 263
|
|
|
277 264 <span class="i">$OptionsInfo</span>{<span class="w">NewTextFile</span>} = <span class="i">$NewTextFile</span><span class="sc">;</span>
|
|
|
278 265 <span class="s">}</span>
|
|
|
279 266
|
|
|
280 267 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
|
|
|
281 <a name="SetupScriptUsage-"></a> 268 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
|
|
|
282 269
|
|
|
283 270 <span class="c"># Retrieve all the options...</span>
|
|
|
284 271 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
285 272 <span class="i">$Options</span>{<span class="w">label</span>} = <span class="q">"yes"</span><span class="sc">;</span>
|
|
|
286 273 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">"comma"</span><span class="sc">;</span>
|
|
|
287 274 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">"comma"</span><span class="sc">;</span>
|
|
|
288 275 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">"yes"</span><span class="sc">;</span>
|
|
|
289 276 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"fast|f"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"indelim=s"</span><span class="cm">,</span> <span class="q">"label|l=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
290 277 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
|
|
|
291 278 <span class="s">}</span>
|
|
|
292 279 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
293 280 <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>
|
|
|
294 281 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
|
|
|
295 282 <span class="s">}</span>
|
|
|
296 283 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
299 286 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n"</span><span class="sc">;</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
302 289 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
|
|
|
303 290 <span class="s">}</span>
|
|
|
304 291 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
305 292 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
|
|
|
306 293 <span class="s">}</span>
|
|
|
307 294 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">label</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
308 295 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{label}, for option \"-l --label\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297 <span class="s">}</span>
|
|
|
311 298
|
|
|
312 <a name="EOF-"></a></pre>
|
|
|
313 <p> </p>
|
|
|
314 <br />
|
|
|
315 <center>
|
|
|
316 <img src="../../../images/h2o2.png">
|
|
|
317 </center>
|
|
|
318 </body>
|
|
|
319 </html>
|
