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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: SortTextFiles.pl,v $
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4 # $Date: 2015/02/28 20:46:21 $
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5 # $Revision: 1.36 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use FindBin; use lib "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37
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38 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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39
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40 # Autoflush STDOUT
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41 $| = 1;
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42
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43 # Starting message...
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44 $ScriptName = basename($0);
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45 print "\n$ScriptName: Starting...\n\n";
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46 $StartTime = new Benchmark;
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47
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48 # Get the options and setup script...
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49 SetupScriptUsage();
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50 if ($Options{help} || @ARGV < 1) {
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51 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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52 }
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53
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54 my(@TextFilesList);
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55 @TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
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56
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57 print "Processing options...\n";
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58 my(%OptionsInfo);
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59 ProcessOptions();
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60
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61 print "Checking input text file(s)...\n";
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62 my(%TextFilesInfo);
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63 RetrieveTextFilesInfo();
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64 ProcessColumnsInfo();
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65
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66 # Generate output files...
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67 my($FileIndex);
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68 if (@TextFilesList > 1) {
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69 print "\nProcessing text files...\n";
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70 }
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71 for $FileIndex (0 .. $#TextFilesList) {
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72 if ($TextFilesInfo{FileOkay}[$FileIndex]) {
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73 print "\nProcessing file $TextFilesList[$FileIndex]...\n";
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74 SortTextFile($FileIndex);
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75 }
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76 }
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77 print "\n$ScriptName:Done...\n\n";
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78
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79 $EndTime = new Benchmark;
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80 $TotalTime = timediff ($EndTime, $StartTime);
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81 print "Total time: ", timestr($TotalTime), "\n";
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82
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83 ###############################################################################
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84
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85 # Sort it out...
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86 sub SortTextFile {
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87 my($Index) = @_;
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88 my($TextFile, $NewTextFile, $KeyCol, $Line, $KeyColValue, $InDelim, @ColLabels, @LineWords);
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89
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90 $TextFile = $TextFilesList[$Index];
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91 $InDelim = $TextFilesInfo{InDelim}[$Index];
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92 $NewTextFile = $TextFilesInfo{OutFile}[$Index];
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93 $KeyCol = $TextFilesInfo{KeyColNum}[$Index];
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94 @ColLabels = @{$TextFilesInfo{ColLabels}[$Index]};
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95
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96 print "Generating new Text file $NewTextFile...\n";
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97 open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n";
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98 open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n";
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99
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100 # Skip over column labels from old file...
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101 $Line = GetTextLine(\*TEXTFILE);
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102
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103 # Add column lablels in new file...
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104 $Line = JoinWords(\@ColLabels, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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105 print NEWTEXTFILE "$Line\n";
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106
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107 # Go over all rows and store the lines using key value as hash...
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108 my(%KeyToLinesMap, @InvalidDataLines, $LineCount);
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109
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110 %KeyToLinesMap = ();
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111 @InvalidDataLines = ();
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112 $LineCount = 1;
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113 TEXTLINE: while ($Line = GetTextLine(\*TEXTFILE)) {
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114 @LineWords = quotewords($InDelim, 0, $Line);
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115 $LineCount++;
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116 if ($KeyCol < @LineWords) {
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117 $KeyColValue = $LineWords[$KeyCol];
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118 if (!IsNotEmpty($KeyColValue)) {
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119 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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120 push @InvalidDataLines, $Line;
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121 if ($OptionsInfo{DetailLevel} >= 3 ) {
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122 print "Ignoring line $LineCount: Contains empty value for key column $ColLabels[$KeyCol]: $Line\n";
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123 }
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124 elsif ($OptionsInfo{DetailLevel} >= 2) {
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125 print "Ignoring line $LineCount: Contains empty value for key column $ColLabels[$KeyCol]...\n";
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126 }
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127 next TEXTLINE;
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128 }
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129 if ($OptionsInfo{KeyData} =~ /^numeric$/i) {
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130 if (!IsFloat($KeyColValue)) {
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131 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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132 push @InvalidDataLines, $Line;
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133 if ($OptionsInfo{DetailLevel} >= 3 ) {
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134 print "Line number $LineCount: Contains non-numerical value for key column $ColLabels[$KeyCol]: $Line\n";
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135 }
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136 elsif ($OptionsInfo{DetailLevel} >= 2) {
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137 print "Line number $LineCount: Contains non-numerical value for key column $ColLabels[$KeyCol]...\n";
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138 }
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139 next TEXTLINE;
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140 }
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141 }
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142 if (exists($KeyToLinesMap{$KeyColValue})) {
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143 # Append to existing line...
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144 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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145 $KeyToLinesMap{$KeyColValue} .= "\n" . $Line;
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146 }
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147 else {
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148 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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149 $KeyToLinesMap{$KeyColValue} = $Line;
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150 }
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151 }
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152 }
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153 if ($OptionsInfo{Sort} =~ /^ascending$/i) {
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154 if ($OptionsInfo{KeyData} =~ /^alphanumeric$/i) {
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155 for $KeyColValue (sort { lc($a) cmp lc($b) } keys %KeyToLinesMap ) {
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156 print NEWTEXTFILE "$KeyToLinesMap{$KeyColValue}\n";
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157 }
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158 }
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159 else {
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160 for $KeyColValue (sort { $a <=> $b } keys %KeyToLinesMap ) {
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161 print NEWTEXTFILE "$KeyToLinesMap{$KeyColValue}\n";
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162 }
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163 }
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164 }
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165 else {
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166 if ($OptionsInfo{KeyData} =~ /^alphanumeric$/i) {
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167 for $KeyColValue (sort { lc($b) cmp lc($a) } keys %KeyToLinesMap ) {
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168 print NEWTEXTFILE "$KeyToLinesMap{$KeyColValue}\n";
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169 }
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170 }
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171 else {
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172 for $KeyColValue (sort { $b <=> $a } keys %KeyToLinesMap ) {
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173 print NEWTEXTFILE "$KeyToLinesMap{$KeyColValue}\n";
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174 }
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175 }
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176 }
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177 # Write out the lines with invalid data...
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178 if (@InvalidDataLines) {
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179 print "Placing ", scalar(@InvalidDataLines)," line(s) with invalid column key data at the end...\n";
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180 for $Line (@InvalidDataLines) {
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181 print NEWTEXTFILE "$Line\n";
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182 }
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183 }
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184 close NEWTEXTFILE;
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185 close TEXTFILE;
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186
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187 }
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188
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189 # Retrieve information about input text files...
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190 sub RetrieveTextFilesInfo {
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191 my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, @ColLabels, $OutFileRoot, $OutFile, $ColNum, $ColLabel);
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192
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193 %TextFilesInfo = ();
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194
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195 @{$TextFilesInfo{FileOkay}} = ();
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196 @{$TextFilesInfo{ColCount}} = ();
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197 @{$TextFilesInfo{ColLabels}} = ();
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198 @{$TextFilesInfo{ColLabelToNumMap}} = ();
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199 @{$TextFilesInfo{InDelim}} = ();
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200 @{$TextFilesInfo{OutFile}} = ();
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201
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202 FILELIST: for $Index (0 .. $#TextFilesList) {
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203 $TextFile = $TextFilesList[$Index];
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204
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205 $TextFilesInfo{FileOkay}[$Index] = 0;
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206 $TextFilesInfo{ColCount}[$Index] = 0;
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207 $TextFilesInfo{InDelim}[$Index] = "";
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208 $TextFilesInfo{OutFile}[$Index] = "";
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209 @{$TextFilesInfo{ColLabels}[$Index]} = ();
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210 %{$TextFilesInfo{ColLabelToNumMap}[$Index]} = ();
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211
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212 if (!(-e $TextFile)) {
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213 warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
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214 next FILELIST;
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215 }
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216 if (!CheckFileType($TextFile, "csv tsv")) {
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217 warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
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218 next FILELIST;
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219 }
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220 ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
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221 if ($FileExt =~ /^tsv$/i) {
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222 $InDelim = "\t";
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223 }
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224 else {
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225 $InDelim = "\,";
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226 if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
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227 warn "Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n";
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228 next FILELIST;
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229 }
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230 if ($Options{indelim} =~ /^semicolon$/i) {
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231 $InDelim = "\;";
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232 }
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233 }
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234
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235 if (!open TEXTFILE, "$TextFile") {
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236 warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
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237 next FILELIST;
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238 }
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239
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240 $Line = GetTextLine(\*TEXTFILE);
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241 @ColLabels = quotewords($InDelim, 0, $Line);
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242 close TEXTFILE;
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243
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244 $FileDir = ""; $FileName = ""; $FileExt = "";
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245 ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
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246 $FileExt = "csv";
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247 if ($Options{outdelim} =~ /^tab$/i) {
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248 $FileExt = "tsv";
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249 }
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250 if ($Options{root} && (@TextFilesList == 1)) {
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251 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
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252 if ($RootFileName && $RootFileExt) {
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253 $FileName = $RootFileName;
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254 }
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255 else {
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256 $FileName = $Options{root};
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257 }
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258 $OutFileRoot = $FileName;
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259 }
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260 else {
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261 $OutFileRoot = $FileName . "SortedByColumn";
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262 }
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263
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264 $OutFile = $OutFileRoot . ".$FileExt";
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265 if (lc($OutFile) eq lc($TextFile)) {
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266 warn "Warning: Ignoring file $TextFile:Output file name, $OutFile, is same as input text file name, $TextFile\n";
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267 next FILELIST;
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268 }
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269 if (!$Options{overwrite}) {
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270 if (-e $OutFile) {
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271 warn "Warning: Ignoring file $TextFile: The file $OutFile already exists\n";
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272 next FILELIST;
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273 }
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274 }
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275
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276 $TextFilesInfo{FileOkay}[$Index] = 1;
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277 $TextFilesInfo{InDelim}[$Index] = $InDelim;
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278 $TextFilesInfo{OutFile}[$Index] = "$OutFile";
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279
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280 $TextFilesInfo{ColCount}[$Index] = @ColLabels;
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281 push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
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282 for $ColNum (0 .. $#ColLabels) {
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283 $ColLabel = $ColLabels[$ColNum];
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284 $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel} = $ColNum;
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285 }
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286 }
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287
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288 }
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289
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290 # Make sure specified key column are okay...
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291 sub ProcessColumnsInfo {
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292 my($Index, $TextFile, $SpecifiedKeyCol);
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293
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294 @{$TextFilesInfo{KeyColNum}} = ();
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295
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296 $SpecifiedKeyCol = $OptionsInfo{SpecifiedKeyCol};
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297
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298 FILELIST: for $Index (0 .. $#TextFilesList) {
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299 $TextFile = $TextFilesList[$Index];
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300 $TextFilesInfo{KeyColNum}[$Index] = 0;
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301
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302 if ($TextFilesInfo{FileOkay}[$Index]) {
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303 my($KeyColNum, $KeyColValid);
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304
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305 $KeyColNum = 0;
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306 $KeyColValid = 1;
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307 if ($SpecifiedKeyCol) {
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308 if ($OptionsInfo{Mode} =~ /^colnum$/i) {
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309 if ($SpecifiedKeyCol <= $TextFilesInfo{ColCount}[$Index]) {
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310 $KeyColNum = $SpecifiedKeyCol - 1;
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311 }
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312 else {
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313 $KeyColValid = 0;
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314 }
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315 }
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316 else {
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317 if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedKeyCol})) {
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318 $KeyColNum = $TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedKeyCol};
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319 }
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320 else {
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321 $KeyColValid = 0;
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322 }
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323 }
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324 }
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325 if ($KeyColValid) {
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326 $TextFilesInfo{KeyColNum}[$Index] = $KeyColNum;
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327 }
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328 else {
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329 warn "Warning: Ignoring file $TextFile: Column key specified, $SpecifiedKeyCol, using \"k --key\" option doesn't exist\n";
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330 $TextFilesInfo{FileOkay}[$Index] = 0;
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331 }
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332 }
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333 }
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334 }
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335
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336 # Process option values...
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337 sub ProcessOptions {
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338 %OptionsInfo = ();
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339
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340 $OptionsInfo{Mode} = $Options{mode};
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341
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342 $OptionsInfo{DetailLevel} = $Options{detail};
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343
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344 $OptionsInfo{Sort} = $Options{sort};
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345 $OptionsInfo{KeyData} = $Options{keydata};
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346
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347 $OptionsInfo{InDelim} = $Options{indelim};
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348
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349 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
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350 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
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351
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352 $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
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353 $OptionsInfo{Root} = defined $Options{root} ? $Options{root} : undef;
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354
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355 $OptionsInfo{Key} = defined $Options{key} ? $Options{key} : undef;
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356 $OptionsInfo{SpecifiedKeyCol} = "";
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357
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358 if (defined $Options{key}) {
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359 $OptionsInfo{SpecifiedKeyCol} = $Options{key};
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360 if ($Options{mode} =~ /^colnum$/i) {
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361 if (!IsPositiveInteger($OptionsInfo{SpecifiedKeyCol})) {
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362 die "Error: Invalid value $Options{key} specified using \"-k --key\" option: Allowed values: > 0\n";
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363 }
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364 }
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365 }
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366 }
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367
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368 # Setup script usage and retrieve command line arguments specified using various options...
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369 sub SetupScriptUsage {
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370 %Options = ();
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371
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372 $Options{detail} = 1;
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373 $Options{mode} = "colnum";
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374 $Options{sort} = "ascending";
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375 $Options{keydata} = "numeric";
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376 $Options{indelim} = "comma";
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377 $Options{outdelim} = "comma";
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378 $Options{quote} = "yes";
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379 if (!GetOptions(\%Options, "detail|d=i", "help|h", "indelim=s", "key|k=s", "keydata=s", "mode|m=s", "outdelim=s", "overwrite|o", "quote|q=s", "root|r=s", "sort|s=s", "workingdir|w=s")) {
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380 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
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381 }
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382 if ($Options{workingdir}) {
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383 if (! -d $Options{workingdir}) {
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384 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
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385 }
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386 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
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387 }
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388 if ($Options{mode} !~ /^(colnum|collabel)$/i) {
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389 die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: colnum or collabel\n";
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390 }
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391 if ($Options{keydata} !~ /^(numeric|alphanumeric)$/i) {
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392 die "Error: The value specified, $Options{keydata}, for option \"--keydata\" is not valid. Allowed values: numeric or alphanumeric\n";
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393 }
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394 if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
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395 die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n";
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396 }
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397 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
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398 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
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399 }
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400 if ($Options{quote} !~ /^(yes|no)$/i) {
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401 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
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402 }
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403 if ($Options{sort} !~ /^(ascending|descending)$/i) {
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404 die "Error: The value specified, $Options{sort}, for option \"-s --sort\" is not valid. Allowed values: ascending or descending\n";
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405 }
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406 if (!IsPositiveInteger($Options{detail})) {
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407 die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
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408 }
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409 }
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410
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411 __END__
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412
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413 =head1 NAME
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414
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415 SortTextFiles.pl - Sort TextFile(s) using values for a column
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416
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417 =head1 SYNOPSIS
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418
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419 SortTextFiles.pl TextFile(s)...
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420
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421 SortTextFiles.pl [B<-d, --detail> infolevel] [B<-h, --help>] [B<--indelim> comma | semicolon] [B<-k, --key> colnum | collabel]
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422 [B<--keydata> numeric | alphanumeric] [B<-m, --mode> colnum | collabel] [B<-o, --overwrite>]
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423 [B<--outdelim> comma | tab | semicolon] [B<-q, --quote> yes | no] [B<-r, --root> rootname]
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424 [B<-s, --sort> ascending | descending] [B<-w, --workingdir> dirname] TextFile(s)...
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425
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426 =head1 DESCRIPTION
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427
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428 Sort I<TextFile(s)> using values for a key column specified by a column number or label.
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429 Only one column key can be specified for sorting. In an event of conflict during sorting
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430 process, two similar values for a column key are simply transferred to output files in
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431 order of their presence in input files. Additionally, rows with empty or inappropriate
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432 values for column key are simply placed at the end. The file names are separated by space.
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433 The valid file extensions are I<.csv> and I<.tsv> for comma/semicolon and tab delimited
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434 text files respectively. All other file names are ignored. All the text files in a
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435 current directory can be specified by I<*.csv>, I<*.tsv>, or the current directory
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436 name. The B<--indelim> option determines the format of I<TextFile(s)>. Any file
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437 which doesn't correspond to the format indicated by B<--indelim> option is ignored.
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438
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439 =head1 OPTIONS
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440
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441 =over 4
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442
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443 =item B<-d, --detail> I<infolevel>
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444
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445 Level of information to print about lines being ignored. Default: I<1>. Possible values:
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446 I<1, 2 or 3>.
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447
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448 =item B<-h, --help>
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449
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450 Print this help message.
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451
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452 =item B<--indelim> I<comma | semicolon>
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453
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454 Input delimiter for CSV I<TextFile(s)>. Possible values: I<comma or semicolon>.
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455 Default value: I<comma>. For TSV files, this option is ignored and I<tab> is used as a
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456 delimiter.
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457
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458 =item B<-k, --key> I<col number | col name>
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459
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460 This value is mode specific. It specifies which column to use for sorting I<TextFile(s)>.
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461 Possible values: I<col number or col label>. Default value: I<first column>.
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462
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463 =item B<--keydata> I<numeric | alphanumeric>
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464
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465 Data type for column key. Possible values: I<numeric or alphanumeric>. Default value:
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466 I<numeric>. For I<alphanumeric> data values, comparison is case insensitive.
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467
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468 =item B<-m, --mode> I<colnum | collabel>
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469
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470 Specify how to sort text files: using column number or column label.
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471 Possible values: I<colnum or collabel>. Default value: I<colnum>.
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472
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473 =item B<-o, --overwrite>
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474
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475 Overwrite existing files.
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476
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477 =item B<--outdelim> I<comma | tab | semicolon>
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478
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479 Output text file delimiter. Possible values: I<comma, tab, or semicolon>
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480 Default value: I<comma>.
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481
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482 =item B<-q, --quote> I<yes | no>
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483
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|
484 Put quotes around column values in output text file. Possible values: I<yes or
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|
485 no>. Default value: I<yes>.
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486
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487 =item B<-r, --root> I<rootname>
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488
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489 New text file name is generated using the root: <Root>.<Ext>. Default new file
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|
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490 name: <InitialTextFileName>SortedByColumn.<Ext>. The csv, and tsv
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|
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491 <Ext> values are used for comma/semicolon, and tab delimited text files
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|
|
492 respectively. This option is ignored for multiple input files.
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|
|
493
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|
|
494 =item B<-s, --sort> I<ascending | descending>
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|
|
495
|
|
|
496 Sorting order for column values. Possible values: I<ascending or descending>.
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|
|
497 Default value: I<ascending>.
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|
|
498
|
|
|
499 =item B<-w, --workingdir> I<dirname>
|
|
|
500
|
|
|
501 Location of working directory. Default: current directory.
|
|
|
502
|
|
|
503 =back
|
|
|
504
|
|
|
505 =head1 EXAMPLES
|
|
|
506
|
|
|
507 To perform numerical sort in ascending order using first column values and generate
|
|
|
508 a new CSV text file NewSample1.csv, type:
|
|
|
509
|
|
|
510 % SortTextFiles.pl -o -r NewSample1 Sample1.csv
|
|
|
511
|
|
|
512 To perform numerical sort in descending order using MolWeight column and generate
|
|
|
513 a new CSV text file NewSample1.csv, type:
|
|
|
514
|
|
|
515 % SortTextFiles.pl -m collabel -k MolWeight --keydata numeric
|
|
|
516 -s descending -r NewSample1 -o Sample1.csv
|
|
|
517
|
|
|
518 To perform numerical sort in ascending order using column number 1 and generate
|
|
|
519 a new TSV text file NewSample1.csv, type:
|
|
|
520
|
|
|
521 % SortTextFiles.pl -m colnum -k 1 --keydata numeric -s ascending
|
|
|
522 -r NewSample1 --outdelim tab -o Sample1.csv
|
|
|
523
|
|
|
524 =head1 AUTHOR
|
|
|
525
|
|
|
526 Manish Sud <msud@san.rr.com>
|
|
|
527
|
|
|
528 =head1 SEE ALSO
|
|
|
529
|
|
|
530 JoinTextFiles.pl, MergeTextFilesWithSD.pl, ModifyTextFilesFormat.pl, SplitTextFiles.pl, TextFilesToHTML.pl
|
|
|
531
|
|
|
532 =head1 COPYRIGHT
|
|
|
533
|
|
|
534 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
535
|
|
|
536 This file is part of MayaChemTools.
|
|
|
537
|
|
|
538 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
539 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
540 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
541 any later version.
|
|
|
542
|
|
|
543 =cut
|
