1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: JoinTextFiles.pl,v $ 4 # $Date: 2008/01/30 21:44:48 $ 5 # $Revision: 1.18 $ 6 # 7 # Author: Manish Sud <msud@san.rr.com> 8 # 9 # Copyright (C) 2004-2008 Manish Sud. All rights reserved. 10 # 11 # This file is part of MayaChemTools. 12 # 13 # MayaChemTools is free software; you can redistribute it and/or modify it under 14 # the terms of the GNU Lesser General Public License as published by the Free 15 # Software Foundation; either version 3 of the License, or (at your option) any 16 # later version. 17 # 18 # MayaChemTools is distributed in the hope that it will be useful, but without 19 # any warranty; without even the implied warranty of merchantability of fitness 20 # for a particular purpose. See the GNU Lesser General Public License for more 21 # details. 22 # 23 # You should have received a copy of the GNU Lesser General Public License 24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or 25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, 26 # Boston, MA, 02111-1307, USA. 27 # 28 29 use 5.006; 30 use strict; 31 use FindBin; use lib "$FindBin::Bin/../lib"; 32 use Getopt::Long; 33 use File::Basename; 34 use Text::ParseWords; 35 use Benchmark; 36 use SDFileUtil; 37 use FileUtil; 38 use TextUtil; 39 40 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 41 my($TextFile, @TextFilesList, $Index, $NewTextFile, $OutQuote, $InDelim, $OutDelim, $FileDir, $FileName, $FileExt, $Line, @Words, $ColLabelsLine, @ColLabels, $NewColLabelsLine, @NewColLabels); 42 43 # Autoflush STDOUT 44 $| = 1; 45 46 # Starting message... 47 $ScriptName = basename $0; 48 print "\n$ScriptName:Starting...\n\n"; 49 $StartTime = new Benchmark; 50 51 # Get the options and setup script... 52 SetupScriptUsage(); 53 if ($Options{help} || @ARGV < 1) { 54 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 55 } 56 @TextFilesList = ExpandFileNames(\@ARGV, "csv tsv"); 57 58 if (@TextFilesList == 1) { 59 die "Error: Specify more than one Text file.\n"; 60 } 61 62 if ($Options{root}) { 63 $FileDir = ""; $FileName = ""; $FileExt = ""; 64 ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root}); 65 if ($FileName && $FileExt) { 66 $NewTextFile = $FileName; 67 } 68 else { 69 $NewTextFile = $Options{root}; 70 } 71 } 72 else { 73 $FileDir = ""; $FileName = ""; $FileExt = ""; 74 ($FileDir, $FileName, $FileExt) = ParseFileName($TextFilesList[0]); 75 $NewTextFile = $FileName . "1To" . @TextFilesList . "Joined"; 76 } 77 if ($Options{outdelim} =~ /^tab$/i) { 78 $NewTextFile .= ".tsv"; 79 } 80 else { 81 $NewTextFile .= ".csv"; 82 } 83 if (!$Options{overwrite}) { 84 if (-e $NewTextFile) { 85 die "Error: The file $NewTextFile already exists.\n"; 86 } 87 } 88 if ($Options{root}) { 89 for $Index (0 .. $#TextFilesList) { 90 if (lc($NewTextFile) eq lc($TextFilesList[$Index])) { 91 die "Error: Output filename, $NewTextFile, is similar to a input file name.\nSpecify a different name using \"-r --root\" option or use default name.\n"; 92 } 93 } 94 } 95 print "Generating new Text file $NewTextFile...\n"; 96 97 # Go over each text file and check consistency of data: same number of columns, 98 # presenece/absence of column labels, and input delimiter which makes sense for 99 # the file extension. And afterwards, join these files appropriately. 100 101 open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n"; 102 $NewColLabelsLine = ""; 103 @NewColLabels = (); 104 FILELIST: for $Index (0 .. $#TextFilesList) { 105 $TextFile = $TextFilesList[$Index]; 106 print "\nProcessing file $TextFile...\n"; 107 if (!(-e $TextFile)) { 108 warn "Warning: Ignoring file $TextFile: It doesn't exist\n"; 109 next FILELIST; 110 } 111 if (!$Options{fast}) { 112 if (!CheckFileType($TextFile, "csv tsv")) { 113 warn "Warning: Ignoring file $TextFile: It's not a text file\n"; 114 next FILELIST; 115 } 116 ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile); 117 if ($FileExt =~ /^tsv$/i) { 118 $InDelim = "\t"; 119 } 120 else { 121 $InDelim = "\,"; 122 if ($Options{indelim} !~ /^(comma|semicolon)$/i) { 123 warn "Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n"; 124 next FILELIST; 125 } 126 if ($Options{indelim} =~ /^semicolon$/i) { 127 $InDelim = "\;"; 128 } 129 } 130 } 131 if (!open TEXTFILE, "$TextFile") { 132 warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n"; 133 next FILELIST; 134 } 135 if ($Options{label} =~ /^yes$/i) { 136 if ($Options{fast}) { 137 $ColLabelsLine = GetTextLine(\*TEXTFILE); 138 if (!$NewColLabelsLine) { 139 $NewColLabelsLine = $ColLabelsLine; 140 print NEWTEXTFILE "$NewColLabelsLine\n"; 141 } 142 } 143 else { 144 $Line = GetTextLine(\*TEXTFILE); 145 if ($NewColLabelsLine) { 146 @ColLabels = quotewords($InDelim, 0, $Line); 147 if (@ColLabels != @NewColLabels) { 148 warn "Warning: Ignoring file $TextFile: The number of columns in this file, ", scalar(@ColLabels), ", is different from the number of columns, ", scalar(@NewColLabels), ", in the first valid text file. \n"; 149 next FILELIST; 150 } 151 $ColLabelsLine = JoinWords(\@ColLabels, $OutDelim, $OutQuote); 152 if ($ColLabelsLine ne $NewColLabelsLine) { 153 warn "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: $NewColLabelsLine \nColumnlabels in current text file: $ColLabelsLine\n"; 154 next FILELIST; 155 } 156 } 157 else { 158 @NewColLabels = quotewords($InDelim, 0, $Line); 159 $NewColLabelsLine = JoinWords(\@NewColLabels, $OutDelim, $OutQuote); 160 print NEWTEXTFILE "$NewColLabelsLine\n"; 161 } 162 } 163 } 164 while ($Line = GetTextLine(\*TEXTFILE)) { 165 if (!$Options{fast}) { 166 @Words = quotewords($InDelim, 0, $Line); 167 $Line = JoinWords(\@Words, $OutDelim, $OutQuote); 168 } 169 print NEWTEXTFILE "$Line\n"; 170 } 171 close TEXTFILE; 172 } 173 close NEWTEXTFILE; 174 175 print "$ScriptName:Done...\n\n"; 176 177 $EndTime = new Benchmark; 178 $TotalTime = timediff ($EndTime, $StartTime); 179 print "Total time: ", timestr($TotalTime), "\n"; 180 181 ############################################################################### 182 183 # Setup script usage and retrieve command line arguments specified using various options... 184 sub SetupScriptUsage { 185 186 # Retrieve all the options... 187 %Options = (); 188 $Options{label} = "yes"; 189 $Options{indelim} = "comma"; 190 $Options{outdelim} = "comma"; 191 $Options{quote} = "yes"; 192 if (!GetOptions(\%Options, "fast|f", "help|h", "indelim=s", "label|l=s", "outdelim=s", "overwrite|o", "quote|q=s", "root|r=s", "workingdir|w=s")) { 193 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 194 } 195 if ($Options{workingdir}) { 196 if (! -d $Options{workingdir}) { 197 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 198 } 199 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 200 } 201 if ($Options{indelim} !~ /^(comma|semicolon)$/i) { 202 die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n"; 203 } 204 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 205 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 206 } 207 if ($Options{quote} !~ /^(yes|no)$/i) { 208 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 209 } 210 if ($Options{label} !~ /^(yes|no)$/i) { 211 die "Error: The value specified, $Options{label}, for option \"-l --label\" is not valid. Allowed values: yes or no\n"; 212 } 213 $OutDelim = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,"); 214 $OutQuote = ($Options{quote} =~ /^yes$/i) ? 1 : 0; 215 } 216