MayaChemTools

   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