       1 #!/usr/bin/perl -w
       2 #
       3 # File: MergeTextFilesWithSD.pl
       4 # Author: Manish Sud <msud@san.rr.com>
       5 #
       6 # Copyright (C) 2018 Manish Sud. All rights reserved.
       7 #
       8 # This file is part of MayaChemTools.
       9 #
      10 # MayaChemTools is free software; you can redistribute it and/or modify it under
      11 # the terms of the GNU Lesser General Public License as published by the Free
      12 # Software Foundation; either version 3 of the License, or (at your option) any
      13 # later version.
      14 #
      15 # MayaChemTools is distributed in the hope that it will be useful, but without
      16 # any warranty; without even the implied warranty of merchantability of fitness
      17 # for a particular purpose.  See the GNU Lesser General Public License for more
      18 # details.
      19 #
      20 # You should have received a copy of the GNU Lesser General Public License
      21 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
      22 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
      23 # Boston, MA, 02111-1307, USA.
      24 #
      25
      26 use strict;
      27 use FindBin; use lib "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Text::ParseWords;
      31 use Benchmark;
      32 use FileHandle;
      33 use SDFileUtil;
      34 use FileUtil;
      35 use TextUtil;
      36
      37 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      38
      39 # Autoflush STDOUT
      40 $| = 1;
      41
      42 # Starting message...
      43 $ScriptName = basename $0;
      44 print "\n$ScriptName:Starting...\n\n";
      45 $StartTime = new Benchmark;
      46
      47 # Get the options and setup script...
      48 SetupScriptUsage();
      49 if ($Options{help} || @ARGV < 1) {
      50   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      51 }
      52
      53 my($SDFile, @TextFilesList);
      54 @TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
      55
      56 if (@TextFilesList < 2) {
      57   die "Error: Specify one or more text files.\n";
      58 }
      59 $SDFile = shift @TextFilesList;
      60
      61 # Process options...
      62 print "Processing options...\n";
      63 my(%OptionsInfo);
      64 ProcessOptions();
      65
      66 # Setup information about input files...
      67 print "Checking input SD and text files...\n";
      68 my(%TextFilesInfo);
      69 ProcessSDFileInfo();
      70 RetrieveTextFilesInfo();
      71 RetrieveColumnsAndKeysInfo();
      72
      73 # Merge files...
      74 print "\nGenerating new SD file $OptionsInfo{NewSDFile}...\n";
      75 MergeTextFilesWithSD();
      76
      77 print "\n$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 # Merge all valid Text files with SD file...
      86 sub MergeTextFilesWithSD {
      87   my($Index, $Line);
      88
      89   open NEWSDFILE, ">$OptionsInfo{NewSDFile}" or die "Error: Couldn't open $OptionsInfo{NewSDFile}: $! \n";
      90
      91   open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
      92
      93   @{$TextFilesInfo{FileHandle}} = ();
      94   for $Index (0 .. $#TextFilesList) {
      95     $TextFilesInfo{FileHandle}[$Index] = new FileHandle;
      96
      97     open $TextFilesInfo{FileHandle}[$Index], "$TextFilesList[$Index]" or die "Error: Couldn't open $TextFilesList[$Index]: $! \n";
      98     GetTextLine($TextFilesInfo{FileHandle}[$Index]);
      99   }
     100
     101   if ($OptionsInfo{Keys}) {
     102     MergeTextColumnValuesUsingKeys(\*NEWSDFILE, \*SDFILE);
     103   }
     104   else {
     105     MergeTextColumnValues(\*NEWSDFILE, \*SDFILE);
     106   }
     107
     108   # Close all opened files...
     109   close NEWSDFILE;
     110   close SDFILE;
     111   for $Index (0 .. $#TextFilesList) {
     112     close $TextFilesInfo{FileHandle}[$Index];
     113   }
     114 }
     115
     116 # Merge the specified text columns into SD file...
     117 sub MergeTextColumnValues {
     118   my($NewSDFileRef, $SDFileRef) = @_;
     119   my($Index, $Value, $CmpdString, $Line, $InDelim, $ColNum, $ColIndex, @ColLabels, @ColValues, @LineWords);
     120
     121   while ($CmpdString = ReadCmpdString($SDFileRef)) {
     122     $CmpdString =~ s/\$\$\$\$$//g;
     123     print $NewSDFileRef "$CmpdString";
     124
     125     # Merge coulmn values from other text files...
     126     @ColLabels = (); @ColValues = ();
     127     for $Index (0 .. $#TextFilesList) {
     128       push @ColLabels, @{$TextFilesInfo{ColToMergeLabels}[$Index]};
     129       $InDelim = $TextFilesInfo{InDelim}[$Index];
     130
     131       if ($Line = GetTextLine($TextFilesInfo{FileHandle}[$Index])) {
     132         @LineWords = quotewords($InDelim, 0, $Line);
     133
     134         for $ColNum (@{$TextFilesInfo{ColToMerge}[$Index]}) {
     135           $Value = ($ColNum < @LineWords) ? $LineWords[$ColNum] : "";
     136           push @ColValues, $Value;
     137         }
     138       }
     139     }
     140
     141     for $ColIndex (0 .. $#ColLabels) {
     142       print $NewSDFileRef "> <$ColLabels[$ColIndex]>\n$ColValues[$ColIndex]\n\n";
     143     }
     144     print $NewSDFileRef "\$\$\$\$\n";
     145   }
     146 }
     147
     148 # Merge the specified text columns into SD file using keys...
     149 sub MergeTextColumnValuesUsingKeys {
     150   my($NewSDFileRef, $SDFileRef) = @_;
     151   my($Index, $CmpdString, $Value, $InDelim, $KeyColNum, $KeyColValue, $Line, $ColIndex, $ColNum, @ColLabels, @ColValues, @LineWords, @CmpdLines, @TextFilesKeysToLinesMap, %DataFieldValues);
     152
     153   # Retrieve text lines from all the text files...
     154   @TextFilesKeysToLinesMap = ();
     155
     156   for $Index (0 .. $#TextFilesList) {
     157     $InDelim = $TextFilesInfo{InDelim}[$Index];
     158     %{$TextFilesKeysToLinesMap[$Index]} = ();
     159     $KeyColNum = $TextFilesInfo{KeysToUse}[$Index];
     160
     161     while ($Line = GetTextLine($TextFilesInfo{FileHandle}[$Index])) {
     162       @LineWords = quotewords($InDelim, 0, $Line);
     163
     164       if ($KeyColNum < @LineWords) {
     165         $KeyColValue = $LineWords[$KeyColNum];
     166
     167         if (length($KeyColValue)) {
     168           if (exists($TextFilesKeysToLinesMap[$Index]{$KeyColValue})) {
     169             warn "Warning: Ignoring line, $Line, in text file $TextFilesList[$Index]: Column key value, $KeyColValue, already exists\n";
     170           }
     171           else {
     172             @{$TextFilesKeysToLinesMap[$Index]{$KeyColValue}} = ();
     173             push @{$TextFilesKeysToLinesMap[$Index]{$KeyColValue}}, @LineWords;
     174           }
     175         }
     176       }
     177     }
     178   }
     179
     180   while ($CmpdString = ReadCmpdString($SDFileRef)) {
     181     @CmpdLines = split "\n", $CmpdString;
     182     %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     183
     184     if (exists($DataFieldValues{$OptionsInfo{SDKey}})) {
     185       @ColLabels = (); @ColValues = ();
     186       $CmpdString =~ s/\$\$\$\$$//g;
     187       print $NewSDFileRef "$CmpdString";
     188
     189       $KeyColValue = $DataFieldValues{$OptionsInfo{SDKey}};
     190
     191       # Merge coulmn values from other text files...
     192       for $Index (0 .. $#TextFilesList) {
     193         push @ColLabels, @{$TextFilesInfo{ColToMergeLabels}[$Index]};
     194         @LineWords = ();
     195
     196         if (exists($TextFilesKeysToLinesMap[$Index]{$KeyColValue})) {
     197           push @LineWords, @{$TextFilesKeysToLinesMap[$Index]{$KeyColValue}};
     198         }
     199
     200         for $ColNum (@{$TextFilesInfo{ColToMerge}[$Index]}) {
     201           $Value = ($ColNum < @LineWords) ? $LineWords[$ColNum] : "";
     202           push @ColValues, $Value;
     203         }
     204       }
     205
     206       for $ColIndex (0 .. $#ColLabels) {
     207         $Value = (($ColIndex < @ColValues) && IsNotEmpty($ColValues[$ColIndex]) ) ? $ColValues[$ColIndex] : "";
     208         print $NewSDFileRef "> <$ColLabels[$ColIndex]>\n$Value\n\n";
     209       }
     210       print $NewSDFileRef "\$\$\$\$\n";
     211     }
     212   }
     213 }
     214
     215 # Retrieve text file columns and keys information for specified options...
     216 sub RetrieveColumnsAndKeysInfo {
     217   ProcessColumnsInfo();
     218
     219   if ($OptionsInfo{Keys}) {
     220     ProcessKeysInfo();
     221   }
     222 }
     223
     224 # Process specified columns...
     225 sub ProcessColumnsInfo {
     226   my($Index, $Values, $ColIndex, $ColNum, $ColLabel, @Words);
     227
     228   @{$TextFilesInfo{ColSpecified}} = ();
     229   @{$TextFilesInfo{ColToMerge}} = ();
     230   @{$TextFilesInfo{ColToMergeLabels}} = ();
     231   @{$TextFilesInfo{ColToMergeNumToLabelMap}} = ();
     232
     233   for $Index (0 .. $#TextFilesList) {
     234
     235     @{$TextFilesInfo{ColSpecified}[$Index]} = ();
     236
     237     $Values = "all";
     238     if ($OptionsInfo{Columns}) {
     239       $Values = $OptionsInfo{ColValues}[$Index];
     240     }
     241
     242     if ($Values =~ /all/i) {
     243       if ($OptionsInfo{Mode} =~ /^colnum$/i) {
     244         for $ColNum (1 .. $TextFilesInfo{ColCount}[$Index]) {
     245           push @{$TextFilesInfo{ColSpecified}[$Index]}, $ColNum;
     246         }
     247       } else {
     248         push @{$TextFilesInfo{ColSpecified}[$Index]}, @{$TextFilesInfo{ColLabels}[$Index]};
     249       }
     250     }
     251     else {
     252       @Words = split ",", $Values;
     253       push @{$TextFilesInfo{ColSpecified}[$Index]}, @Words;
     254     }
     255
     256     @{$TextFilesInfo{ColToMerge}[$Index]} = ();
     257     %{$TextFilesInfo{ColToMergeNumToLabelMap}[$Index]} = ();
     258
     259     if ($OptionsInfo{Mode} =~ /^collabel$/i) {
     260       for $ColIndex (0 .. $#{$TextFilesInfo{ColSpecified}[$Index]}) {
     261         $ColLabel = $TextFilesInfo{ColSpecified}[$Index][$ColIndex];
     262
     263         if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel})) {
     264           $ColNum = $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel};
     265           push @{$TextFilesInfo{ColToMerge}[$Index]}, $ColNum;
     266           $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum} = $ColLabel;
     267         }
     268         else {
     269           warn "Warning: Ignoring value, $ColLabel, specified using \"-c --column\" option: column name doesn't exist in  $TextFilesList[$Index]  \n";
     270         }
     271       }
     272     }
     273     else {
     274       for $ColIndex (0 .. $#{$TextFilesInfo{ColSpecified}[$Index]}) {
     275         $ColNum = $TextFilesInfo{ColSpecified}[$Index][$ColIndex];
     276
     277         # Make sure it's a numeric value...
     278         if (!IsPositiveInteger($ColNum)) {
     279           warn "Warning: Ignoring value, $ColNum, specified using \"-c --column\" option:  Allowed integer values: > 0\n";
     280         }
     281         else {
     282           if ($ColNum > 0 && $ColNum <= $TextFilesInfo{ColCount}[$Index]) {
     283             $ColNum -= 1;
     284             push @{$TextFilesInfo{ColToMerge}[$Index]}, $ColNum;
     285             $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum} = $TextFilesInfo{ColLabels}[$Index][$ColNum];
     286           }
     287           else {
     288             warn "Warning: Ignoring value, $ColNum, specified using \"-c --column\" option: column number doesn't exist in  $TextFilesList[$Index]  \n";
     289           }
     290         }
     291       }
     292     }
     293
     294     my (@TextFilesColToMergeSorted) = sort { $a <=> $b } @{$TextFilesInfo{ColToMerge}[$Index]};
     295
     296     @{$TextFilesInfo{ColToMerge}[$Index]} = ();
     297     push @{$TextFilesInfo{ColToMerge}[$Index]}, @TextFilesColToMergeSorted;
     298
     299     # Set up the labels...
     300     @{$TextFilesInfo{ColToMergeLabels}[$Index]} = ();
     301     for $ColNum (@TextFilesColToMergeSorted) {
     302       push @{$TextFilesInfo{ColToMergeLabels}[$Index]}, $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum};
     303     }
     304   }
     305 }
     306
     307 # Process specified keys....
     308 sub ProcessKeysInfo {
     309   my($Index, $ColNum, $ColLabel, $Key);
     310
     311   @{$TextFilesInfo{KeysSpecified}} = ();
     312   @{$TextFilesInfo{KeysToUse}} = ();
     313
     314   for $Index (0 .. $#TextFilesList) {
     315     $Key = $OptionsInfo{KeyValues}[$Index];
     316
     317     $TextFilesInfo{KeysSpecified}[$Index] = $Key;
     318     $TextFilesInfo{KeysToUse}[$Index] = -1;
     319
     320     if ($OptionsInfo{Mode} =~ /^collabel$/i) {
     321       $ColLabel = $Key;
     322
     323       if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel})) {
     324         $TextFilesInfo{KeysToUse}[$Index] =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel};
     325       }
     326       else {
     327         warn "Warning: Ignoring value, $ColLabel, specified using \"-k --keys\" option: column name doesn't exist in  $TextFilesList[$Index]  \n";
     328       }
     329     }
     330     else {
     331       $ColNum = $Key;
     332       if (!IsPositiveInteger($ColNum)) {
     333         warn "Warning: Ignoring value, $ColNum, specified using \"-k --keys\" option: Allowed integer values: > 0  \n";
     334       }
     335       else {
     336         if ($ColNum > 0 && $ColNum <= $TextFilesInfo{ColCount}[$Index]) {
     337           $TextFilesInfo{KeysToUse}[$Index] = $ColNum - 1;
     338         }
     339         else {
     340           warn "Warning: Ignoring value, $ColNum, specified using \"-k --keys\" option: column number doesn't exist in  $TextFilesList[$Index]  \n";
     341         }
     342       }
     343     }
     344   }
     345
     346   # Modify columns to merge list to make sure the columns identified by key are taken off the list
     347   my(@TextFilesColToMergeFiltered, @TextFilesColToMergeLabelsFiltered);
     348
     349   for $Index (0 .. $#TextFilesList) {
     350     @TextFilesColToMergeFiltered = ();
     351     @TextFilesColToMergeLabelsFiltered = ();
     352
     353     for $ColNum (@{$TextFilesInfo{ColToMerge}[$Index]}) {
     354       if ($TextFilesInfo{KeysToUse}[$Index] != $ColNum) {
     355         push @TextFilesColToMergeFiltered, $ColNum;
     356         push @TextFilesColToMergeLabelsFiltered, $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum};
     357       }
     358     }
     359
     360     @{$TextFilesInfo{ColToMerge}[$Index]} = ();
     361     push @{$TextFilesInfo{ColToMerge}[$Index]}, @TextFilesColToMergeFiltered;
     362
     363     @{$TextFilesInfo{ColToMergeLabels}[$Index]} = ();
     364     push @{$TextFilesInfo{ColToMergeLabels}[$Index]}, @TextFilesColToMergeLabelsFiltered;
     365   }
     366 }
     367
     368 # Check SD file...
     369 sub ProcessSDFileInfo {
     370   if (!CheckFileType($SDFile, "sd sdf")) {
     371     die "Error: Invalid first file $SDFile: It's not a SD file\n";
     372   }
     373   if (!(-e $SDFile)) {
     374     die "Error: SDFile $SDFile doesn't exist\n";
     375   }
     376 }
     377
     378 # Retrieve information about input text files...
     379 sub RetrieveTextFilesInfo {
     380   my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, $ColNum, $ColLabel, $FileNotOkayCount, @ColLabels,);
     381
     382   %TextFilesInfo = ();
     383
     384   @{$TextFilesInfo{FileOkay}} = ();
     385   @{$TextFilesInfo{ColCount}} = ();
     386   @{$TextFilesInfo{ColLabels}} = ();
     387   @{$TextFilesInfo{ColLabelToNumMap}} = ();
     388   @{$TextFilesInfo{InDelim}} = ();
     389
     390   $FileNotOkayCount = 0;
     391
     392   FILELIST: for $Index (0 .. $#TextFilesList) {
     393     $TextFile = $TextFilesList[$Index];
     394
     395     $TextFilesInfo{FileOkay}[$Index] = 0;
     396     $TextFilesInfo{ColCount}[$Index] = 0;
     397     $TextFilesInfo{InDelim}[$Index] = "";
     398
     399     @{$TextFilesInfo{ColLabels}[$Index]} = ();
     400     %{$TextFilesInfo{ColLabelToNumMap}[$Index]} = ();
     401
     402     if (!(-e $TextFile)) {
     403       warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
     404       $FileNotOkayCount++;
     405       next FILELIST;
     406     }
     407     if (!CheckFileType($TextFile, "csv tsv")) {
     408       warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
     409       $FileNotOkayCount++;
     410       next FILELIST;
     411     }
     412     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
     413     if ($FileExt =~ /^tsv$/i) {
     414       $InDelim = "\t";
     415     }
     416     else {
     417       $InDelim = "\,";
     418       if ($OptionsInfo{InDelim} !~ /^(comma|semicolon)$/i) {
     419         warn "Warning: Ignoring file $TextFile: The value specified, $OptionsInfo{InDelim}, for option \"--indelim\" is not valid for csv files\n";
     420         $FileNotOkayCount++;
     421         next FILELIST;
     422       }
     423       if ($OptionsInfo{InDelim} =~ /^semicolon$/i) {
     424         $InDelim = "\;";
     425       }
     426     }
     427
     428     if (!open TEXTFILE, "$TextFile") {
     429       warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
     430       $FileNotOkayCount++;
     431       next FILELIST;
     432     }
     433
     434     $Line = GetTextLine(\*TEXTFILE);
     435     @ColLabels = quotewords($InDelim, 0, $Line);
     436     close TEXTFILE;
     437
     438     $TextFilesInfo{FileOkay}[$Index] = 1;
     439     $TextFilesInfo{InDelim}[$Index] = $InDelim;
     440
     441     $TextFilesInfo{ColCount}[$Index] = @ColLabels;
     442     push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
     443     for $ColNum (0 .. $#ColLabels) {
     444       $ColLabel = $ColLabels[$ColNum];
     445       $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel} = $ColNum;
     446     }
     447   }
     448   # Make sure all specified files are valid for merging to work properly...
     449   if ($FileNotOkayCount) {
     450     die "Error: Problems with input text file(s)...\n";
     451   }
     452 }
     453
     454 # Process option values...
     455 sub ProcessOptions {
     456   my($Index, $FileDir, $FileName, $FileExt, $NewSDFile, @ColValues, @KeyValues);
     457
     458   %OptionsInfo = ();
     459
     460   $OptionsInfo{Mode} = $Options{mode};
     461
     462   $OptionsInfo{Columns} = $Options{columns};
     463   @{$OptionsInfo{ColValues}} = ();
     464
     465   if ($Options{columns}) {
     466     @ColValues = split ";", $Options{columns};
     467     if (@ColValues != @TextFilesList) {
     468       die "Error: Invalid number of values specified by \"-c --columns\" option: it must be equal to number of input text files.\n";
     469     }
     470     for $Index (0 .. $#ColValues) {
     471       if (!length($ColValues[$Index])) {
     472         die "Error: Invalid value specified by \"-c --columns\" option: empty values are not allowed.\n";
     473       }
     474     }
     475     @{$OptionsInfo{ColValues}} = @ColValues;
     476   }
     477
     478   $OptionsInfo{Keys} = $Options{keys};
     479   @{$OptionsInfo{KeyValues}} = ();
     480
     481   if ($Options{keys}) {
     482     @KeyValues = split ";", $Options{keys};
     483     if (@KeyValues != @TextFilesList) {
     484       die "Error: Invalid number of values specified by \"-k --keys\" option: it must be equal to number of input text files.\n";
     485     }
     486     for $Index (0 .. $#KeyValues) {
     487       if (!length($KeyValues[$Index])) {
     488         die "Error: Invalid value specified by \"-k --keys\" option: empty values are not allowed.\n";
     489       }
     490     }
     491     @{$OptionsInfo{KeyValues}} = @KeyValues;
     492   }
     493
     494   $OptionsInfo{InDelim} = $Options{indelim};
     495
     496   $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
     497   $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
     498
     499   $OptionsInfo{SDKey} = defined $Options{sdkey} ? $Options{sdkey} : undef;
     500
     501   # Setup new SD file...
     502   if ($Options{root}) {
     503     $FileDir = ""; $FileName = ""; $FileExt = "";
     504     ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root});
     505     if ($FileName && $FileExt) {
     506       $NewSDFile = $FileName;
     507     }
     508     else {
     509       $NewSDFile =  $Options{root};
     510     }
     511   }
     512   else {
     513     $FileDir = ""; $FileName = ""; $FileExt = "";
     514     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     515
     516     $NewSDFile = $FileName;
     517     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFilesList[0]);
     518
     519     $NewSDFile = $NewSDFile . "MergedWith" . $FileName . "1To" . @TextFilesList;
     520   }
     521
     522   $NewSDFile = $NewSDFile . ".sdf";
     523   if (!$Options{overwrite}) {
     524     if (-e $NewSDFile) {
     525       die "Error: The file $NewSDFile already exists.\n";
     526     }
     527   }
     528   if ($Options{root}) {
     529     if (lc($NewSDFile) eq lc($SDFile)) {
     530       die "Error: Output filename, $NewSDFile, is similar to a input file name.\nSpecify a different name using \"-r --root\" option or use default name.\n";
     531     }
     532   }
     533   $OptionsInfo{NewSDFile} = $NewSDFile;
     534 }
     535
     536 # Setup script usage  and retrieve command line arguments specified using various options...
     537 sub SetupScriptUsage {
     538
     539   # Retrieve all the options...
     540   %Options = ();
     541   $Options{mode} = "colnum";
     542   $Options{indelim} = "comma";
     543
     544   if (!GetOptions(\%Options, "help|h", "indelim=s", "columns|c=s", "keys|k=s", "mode|m=s", "overwrite|o", "root|r=s", "sdkey|s=s", "workingdir|w=s")) {
     545     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     546   }
     547   if ($Options{workingdir}) {
     548     if (! -d $Options{workingdir}) {
     549       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     550     }
     551     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     552   }
     553   if ($Options{mode} !~ /^(colnum|collabel)$/i) {
     554     die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: colnum, or collabel\n";
     555   }
     556   if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
     557     die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n";
     558   }
     559   if ($Options{sdkey} && !$Options{keys}) {
     560     die "Error: The option \"-s --sdkey\" can't be specified without the \"-k --keys\" option.\n";
     561   }
     562   elsif (!$Options{sdkey} && $Options{keys}) {
     563     die "Error: The option \"-k --keys\" can't be specified without the \"-s --sdkey\" option.\n";
     564   }
     565 }
     566