1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: ModifyTextFilesFormat.pl,v $ 4 # $Date: 2015/02/28 20:46:20 $ 5 # $Revision: 1.34 $ 6 # 7 # Author: Manish Sud <msud@san.rr.com> 8 # 9 # Copyright (C) 2015 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 strict; 30 use FindBin; use lib "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Text::ParseWords; 34 use Benchmark; 35 use FileUtil; 36 use TextUtil; 37 38 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 39 40 # Autoflush STDOUT 41 $| = 1; 42 43 # Starting message... 44 $ScriptName = basename $0; 45 print "\n$ScriptName:Starting...\n\n"; 46 $StartTime = new Benchmark; 47 48 # Get the options and setup script... 49 SetupScriptUsage(); 50 if ($Options{help} || @ARGV < 1) { 51 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 52 } 53 54 my(@TextFilesList); 55 @TextFilesList = ExpandFileNames(\@ARGV, "csv tsv"); 56 57 # Process options... 58 print "Processing options...\n"; 59 my(%OptionsInfo); 60 ProcessOptions(); 61 62 print "Checking input text file(s)...\n"; 63 my(%TextFilesInfo); 64 RetrieveTextFilesInfo(); 65 66 # Generate output files... 67 my($FileIndex); 68 if (@TextFilesList > 1) { 69 print "\nProcessing text files...\n"; 70 } 71 for $FileIndex (0 .. $#TextFilesList) { 72 if ($TextFilesInfo{FileOkay}[$FileIndex]) { 73 print "\nProcessing file $TextFilesList[$FileIndex]...\n"; 74 ModifyTextFileFormat($FileIndex); 75 } 76 } 77 print "\n$ScriptName:Done...\n\n"; 78 79 $EndTime = new Benchmark; 80 $TotalTime = timediff ($EndTime, $StartTime); 81 print "Total time: ", timestr($TotalTime), "\n"; 82 83 ############################################################################### 84 85 # Modify text file format... 86 sub ModifyTextFileFormat { 87 my($Index) = @_; 88 my($TextFile, $NewTextFile, $InDelim, $Line, @Words); 89 90 $TextFile = $TextFilesList[$Index]; 91 92 $NewTextFile = $TextFilesInfo{OutFile}[$Index]; 93 $InDelim = $TextFilesInfo{InDelim}[$Index]; 94 95 print "Generating new $NewTextFile file...\n"; 96 97 open NEWTEXTFILE, ">$NewTextFile" or die "Error: Can't open $NewTextFile !$ \n"; 98 open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n"; 99 100 while ($Line = GetTextLine(\*TEXTFILE)) { 101 @Words = quotewords($InDelim, 0, $Line); 102 $Line = JoinWords(\@Words, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote}); 103 print NEWTEXTFILE "$Line\n"; 104 } 105 106 close NEWTEXTFILE; 107 close TEXTFILE; 108 } 109 110 # Retrieve information about input text files... 111 sub RetrieveTextFilesInfo { 112 my($Index, $TextFile, $NewTextFile, $FileDir, $FileName, $FileExt, $InDelim, $OutFileExt); 113 114 %TextFilesInfo = (); 115 @{$TextFilesInfo{FileOkay}} = (); 116 @{$TextFilesInfo{InDelim}} = (); 117 @{$TextFilesInfo{OutFile}} = (); 118 119 FILELIST: for $Index (0 .. $#TextFilesList) { 120 $TextFile = $TextFilesList[$Index]; 121 122 $TextFilesInfo{FileOkay}[$Index] = 0; 123 $TextFilesInfo{InDelim}[$Index] = ""; 124 $TextFilesInfo{OutFile}[$Index] = ""; 125 126 if (!(-e $TextFile)) { 127 warn "Warning: Ignoring file $TextFile: It doesn't exist\n"; 128 next FILELIST; 129 } 130 if (!CheckFileType($TextFile, "csv tsv")) { 131 warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n"; 132 next FILELIST; 133 } 134 if (!open TEXTFILE, "$TextFile") { 135 warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n"; 136 next FILELIST; 137 } 138 close TEXTFILE; 139 140 ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile); 141 142 if ($FileExt =~ /^tsv$/i) { 143 $InDelim = "\t"; 144 } 145 else { 146 $InDelim = "\,"; 147 if ($OptionsInfo{InDelim} !~ /^(comma|semicolon)$/i) { 148 warn "Warning: Ignoring file $TextFile: The value specified, $OptionsInfo{InDelim}, for option \"--indelim\" is not valid for csv files\n"; 149 next FILELIST; 150 } 151 if ($OptionsInfo{InDelim} =~ /^semicolon$/i) { 152 $InDelim = "\;"; 153 } 154 } 155 156 if (lc($InDelim) eq lc($OptionsInfo{OutDelim})) { 157 warn "Warning: Ignoring file $TextFile: The value specified, $Options{outdelim}, for option \"--outdelim\" is same as input delimiter\n"; 158 next FILELIST; 159 } 160 161 $OutFileExt = ($Options{outdelim} =~ /^tab$/i ) ? "tsv" : "csv"; 162 163 $NewTextFile = $FileName; 164 if ($OptionsInfo{OutFileRoot} && (@TextFilesList == 1)) { 165 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); 166 if ($RootFileName && $RootFileExt) { 167 $NewTextFile = $RootFileName; 168 } 169 else { 170 $NewTextFile = $OptionsInfo{OutFileRoot}; 171 } 172 $NewTextFile .= ".$OutFileExt"; 173 } 174 else { 175 $NewTextFile .= "FormatModified" . ".$OutFileExt"; 176 } 177 178 if (!$OptionsInfo{Overwrite}) { 179 if (-e $NewTextFile) { 180 warn "Warning: Ignoring file $TextFile: New Text file, $NewTextFile, already exists\n"; 181 next FILELIST; 182 } 183 } 184 185 $TextFilesInfo{FileOkay}[$Index] = 1; 186 $TextFilesInfo{InDelim}[$Index] = $InDelim; 187 $TextFilesInfo{OutFile}[$Index] = $NewTextFile; 188 } 189 190 } 191 192 # Process option values... 193 sub ProcessOptions { 194 %OptionsInfo = (); 195 196 $OptionsInfo{InDelim} = $Options{indelim}; 197 198 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : undef; 199 $OptionsInfo{Overwrite} = $Options{overwrite} ? $Options{overwrite} : undef; 200 201 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,"); 202 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0; 203 204 } 205 206 # Setup script usage and retrieve command line arguments specified using various options... 207 sub SetupScriptUsage { 208 209 # Retrieve all the options... 210 %Options = (); 211 212 $Options{indelim} = "comma"; 213 $Options{outdelim} = "tab"; 214 $Options{quote} = "yes"; 215 216 if (!GetOptions(\%Options, "help|h", "indelim=s", "outdelim=s", "overwrite|o", "quote|q=s", "root|r=s", "workingdir|w=s")) { 217 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 218 } 219 if ($Options{workingdir}) { 220 if (! -d $Options{workingdir}) { 221 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 222 } 223 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 224 } 225 if ($Options{indelim} !~ /^(comma|semicolon)$/i) { 226 die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n"; 227 } 228 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) { 229 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"; 230 } 231 if ($Options{quote} !~ /^(yes|no)$/i) { 232 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"; 233 } 234 } 235