MayaChemTools

   1 #!/usr/bin/perl -w
   2 #
   3 # $RCSfile: ElementalAnalysisTextFiles.pl,v $
   4 # $Date: 2015/02/28 20:46:19 $
   5 # $Revision: 1.28 $
   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 "$FindBin::Bin/../lib";
  31 use Getopt::Long;
  32 use File::Basename;
  33 use Text::ParseWords;
  34 use Benchmark;
  35 use FileUtil;
  36 use TextUtil;
  37 use MolecularFormula;
  38 
  39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
  40 
  41 # Autoflush STDOUT
  42 $| = 1;
  43 
  44 # Starting message...
  45 $ScriptName = basename($0);
  46 print "\n$ScriptName: Starting...\n\n";
  47 $StartTime = new Benchmark;
  48 
  49 # Get the options and setup script...
  50 SetupScriptUsage();
  51 if ($Options{help} || @ARGV < 1) {
  52   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
  53 }
  54 
  55 my(@TextFilesList);
  56 @TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
  57 
  58 # Process options...
  59 my(%OptionsInfo);
  60 print "Processing options...\n";
  61 ProcessOptions();
  62 
  63 print "Checking input text file(s)...\n";
  64 my(%TextFilesInfo);
  65 RetrieveTextFilesInfo();
  66 RetrieveColumnsAndLabelsInfo();
  67 
  68 # Generate output files...
  69 my($FileIndex);
  70 if (@TextFilesList > 1) {
  71   print "\nProcessing text files...\n";
  72 }
  73 for $FileIndex (0 .. $#TextFilesList) {
  74   if ($TextFilesInfo{FileOkay}[$FileIndex]) {
  75     print "\nProcessing file $TextFilesList[$FileIndex]...\n";
  76     PerformElementalAnalysis($FileIndex);
  77   }
  78 }
  79 print "\n$ScriptName:Done...\n\n";
  80 
  81 $EndTime = new Benchmark;
  82 $TotalTime = timediff ($EndTime, $StartTime);
  83 print "Total time: ", timestr($TotalTime), "\n";
  84 
  85 ###############################################################################
  86 
  87 # Perform elemental analysis...
  88 sub PerformElementalAnalysis {
  89   my($Index) = @_;
  90   my($TextFile, $NewTextFile, $FormulaCol, $Line, $NewLine, $FormulaColValue, $InDelim, $ColNum, $Value, $Status, $ErrorMsg, @ColLabels, @LineWords, @ColNumsBeforeNew, @ColNumsAfterNew);
  91 
  92   $TextFile = $TextFilesList[$Index];
  93   $InDelim = $TextFilesInfo{InDelim}[$Index];
  94   $NewTextFile = $TextFilesInfo{OutFile}[$Index];
  95   $FormulaCol = $TextFilesInfo{FormulaColNum}[$Index];
  96 
  97   @ColNumsBeforeNew = @{$TextFilesInfo{ColNumsBeforeNew}[$Index]};
  98   @ColNumsAfterNew = @{$TextFilesInfo{ColNumsAfterNew}[$Index]};
  99 
 100   print "Generating new Text file $NewTextFile...\n";
 101   open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n";
 102   open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n";
 103 
 104   # Skip over column labels from old file...
 105   $Line = GetTextLine(\*TEXTFILE);
 106 
 107   # Add column lablels in new file...
 108   @ColLabels = ();
 109   for $ColNum (@ColNumsBeforeNew) {
 110     push @ColLabels, $TextFilesInfo{ColLabels}[$Index][$ColNum];
 111   }
 112   for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
 113     push @ColLabels, $TextFilesInfo{ValueLabelsMap}[$Index]{$Value};
 114   }
 115   for $ColNum (@ColNumsAfterNew) {
 116     push @ColLabels, $TextFilesInfo{ColLabels}[$Index][$ColNum];
 117   }
 118   $NewLine = '';
 119   $NewLine = JoinWords(\@ColLabels, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
 120   print NEWTEXTFILE "$NewLine\n";
 121 
 122   # Go over all rows...
 123   my($LineCount, $ElementsRef, $ElementCompositionRef, $CalculationType, $CalculatedValue, @CalculatedValues);
 124 
 125   $LineCount = 1;
 126   TEXTLINE: while ($Line = GetTextLine(\*TEXTFILE)) {
 127     @LineWords = quotewords($InDelim, 0, $Line);
 128     $LineCount++;
 129 
 130     @CalculatedValues = ();
 131     for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
 132       push @CalculatedValues, '';
 133     }
 134     if ($FormulaCol > @LineWords) {
 135       $ErrorMsg = "Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] not found";
 136       PrintErrorMsg($Line, $ErrorMsg);
 137       ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
 138       next TEXTLINE;
 139     }
 140 
 141     # Make sure it's a valid molecular formula...
 142     $FormulaColValue = $LineWords[$FormulaCol];
 143     if ($OptionsInfo{CheckFormula}) {
 144       ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($FormulaColValue);
 145       if (!$Status) {
 146         $ErrorMsg = "Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] value is not valid: $ErrorMsg";
 147         PrintErrorMsg($Line, $ErrorMsg);
 148         ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
 149         next TEXTLINE;
 150       }
 151     }
 152 
 153     # Calculate appropriate values and write 'em out...
 154     @CalculatedValues = ();
 155     for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
 156       if ($CalculationType =~ /^ElementalAnalysis$/i) {
 157         ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($FormulaColValue);
 158         $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
 159       }
 160       elsif ($CalculationType =~ /^MolecularWeight$/i) {
 161         $CalculatedValue = MolecularFormula::CalculateMolecularWeight($FormulaColValue);
 162         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
 163       }
 164       elsif ($CalculationType =~ /^ExactMass$/i) {
 165         $CalculatedValue = MolecularFormula::CalculateExactMass($FormulaColValue);
 166         $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
 167       }
 168       else {
 169         $CalculatedValue = '';
 170       }
 171       push @CalculatedValues, $CalculatedValue;
 172     }
 173 
 174     ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
 175   }
 176   close NEWTEXTFILE;
 177   close TEXTFILE;
 178 
 179 }
 180 
 181 # Write out new line using old and new calculated data...
 182 sub ComposeAndWriteNewLine {
 183   my($NewTextFileRef, $OldLineWordsRef, $ColNumsBeforeNewRef, $ColNumsAfterNewRef, $CalculatedValuesRef) = @_;
 184   my($NewLine, $ColNum, $Value, @NewLineWords);
 185 
 186   @NewLineWords = ();
 187   for $ColNum (@{$ColNumsBeforeNewRef}) {
 188     push @NewLineWords, $OldLineWordsRef->[$ColNum];
 189   }
 190   for $Value (@{$CalculatedValuesRef}) {
 191     push @NewLineWords, $Value;
 192   }
 193   for $ColNum (@{$ColNumsAfterNewRef}) {
 194     push @NewLineWords, $OldLineWordsRef->[$ColNum];
 195   }
 196   $NewLine = JoinWords(\@NewLineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
 197   print $NewTextFileRef "$NewLine\n";
 198 }
 199 
 200 # Print out error message...
 201 sub PrintErrorMsg {
 202   my($Line, $ErrorMsg) = @_;
 203 
 204   if ($OptionsInfo{DetailLevel} >= 2 ) {
 205     print "$ErrorMsg: $Line\n";
 206   }
 207   elsif ($OptionsInfo{DetailLevel} >= 1) {
 208     print "$ErrorMsg\n";
 209   }
 210 }
 211 
 212 # Process formula columns and other information...
 213 sub RetrieveColumnsAndLabelsInfo {
 214   RetrieveFormulaColumnsInfo();
 215   RetrieveStartColumnsAndValueLabelsInfo();
 216 }
 217 
 218 # Make sure specified formula column are okay...
 219 sub RetrieveFormulaColumnsInfo {
 220   my($Index, $TextFile);
 221 
 222   @{$TextFilesInfo{FormulaColNum}} = ();
 223 
 224  FILELIST: for $Index (0 .. $#TextFilesList) {
 225     $TextFile = $TextFilesList[$Index];
 226 
 227     $TextFilesInfo{FormulaColNum}[$Index] = 0;
 228 
 229     if ($TextFilesInfo{FileOkay}[$Index]) {
 230       my($FormulaColNum, $FormulaColValid);
 231 
 232       $FormulaColNum = 0;
 233       $FormulaColValid = 0;
 234       if ($OptionsInfo{SpecifiedFormulaCol}) {
 235         if ($OptionsInfo{ColMode} =~ /^colnum$/i) {
 236           if ($OptionsInfo{SpecifiedFormulaCol} <= $TextFilesInfo{ColCount}[$Index]) {
 237             $FormulaColNum = $OptionsInfo{SpecifiedFormulaCol} - 1;
 238             $FormulaColValid = 1;
 239           }
 240         }
 241         else {
 242           if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$OptionsInfo{SpecifiedFormulaCol}})) {
 243             $FormulaColNum =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$OptionsInfo{SpecifiedFormulaCol}};
 244             $FormulaColValid = 1;
 245           }
 246         }
 247       }
 248       else {
 249         # Grab the first column with the word Formula in its label...
 250         my($ColLabel);
 251         LABEL: for $ColLabel (@{$TextFilesInfo{ColLabels}[$Index]}) {
 252           if ($ColLabel =~ /Formula/i) {
 253             $FormulaColNum =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel};
 254             $FormulaColValid = 1;
 255             last LABEL;
 256           }
 257         }
 258       }
 259       if ($FormulaColValid) {
 260         $TextFilesInfo{FormulaColNum}[$Index] = $FormulaColNum;
 261       }
 262       else {
 263         if ($OptionsInfo{SpecifiedFormulaCol}) {
 264           warn "Warning: Ignoring file $TextFile: Formula column specified, $OptionsInfo{SpecifiedFormulaCol}, using \"f --formulacol\" option doesn't exist\n";
 265         }
 266         else {
 267           warn "Warning: Ignoring file $TextFile: Column label containing the word Formula doesn't exist\n";
 268         }
 269         $TextFilesInfo{FileOkay}[$Index] = 0;
 270       }
 271     }
 272   }
 273 }
 274 
 275 # Setup starting column number for adding calculated values and
 276 # column lables to use for these values...
 277 sub RetrieveStartColumnsAndValueLabelsInfo {
 278   my($Index, $TextFile, $SpecifiedStartColNum, $StartColNum, $Label, $Value, $NewLabel, $Count, $BeforeStartColNum, $AfterStartColNum, $FirstColNum, $LastColNum, $ColNum, $Part1StartColNum, $Part1EndColNum, $Part2StartColNum, $Part2EndColNum, @Part1ColNums, @Part2ColNums);
 279 
 280   # Start column number for inserting new values...
 281   $SpecifiedStartColNum = "last";
 282   if (defined($OptionsInfo{StartCol})) {
 283     if (length($OptionsInfo{StartCol})) {
 284       $SpecifiedStartColNum = $OptionsInfo{StartCol}
 285     }
 286   }
 287 
 288   # Column labels for for new calculated values...
 289   my(%NewValueLabels) = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass');
 290   if (@{$OptionsInfo{SpecifiedValueLabels}}) {
 291     for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueLabels}}; $Index +=2) {
 292       $Value = $OptionsInfo{SpecifiedValueLabels}[$Index];
 293       $Label = $OptionsInfo{SpecifiedValueLabels}[$Index + 1];
 294       if (exists $NewValueLabels{$Value}) {
 295         $NewValueLabels{$Value} = $Label;
 296       }
 297     }
 298   }
 299 
 300   @{$TextFilesInfo{ColNumsBeforeNew}} = ();
 301   @{$TextFilesInfo{ColNumsAfterNew}} = ();
 302   @{$TextFilesInfo{ValueLabelsMap}} = ();
 303 
 304   FILELIST: for $Index (0 .. $#TextFilesList) {
 305     $TextFile = $TextFilesList[$Index];
 306 
 307     @{$TextFilesInfo{ColNumsBeforeNew}[$Index]} = ();
 308     @{$TextFilesInfo{ColNumsAfterNew}[$Index]} = ();
 309     %{$TextFilesInfo{ValueLabelsMap}[$Index]} = ();
 310 
 311     if (!$TextFilesInfo{FileOkay}[$Index]) {
 312       next FILELIST;
 313     }
 314 
 315     if ($SpecifiedStartColNum !~ /^last$/i) {
 316       if ($OptionsInfo{ColMode} =~ /^collabel$/i) {
 317         if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedStartColNum})) {
 318           $StartColNum = $TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedStartColNum};
 319         }
 320         else {
 321           die "Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column name doesn't exist in  $TextFile  \n";
 322         }
 323       }
 324       else {
 325         if ($SpecifiedStartColNum > 0 && $SpecifiedStartColNum <= $TextFilesInfo{ColCount}[$Index]) {
 326           $StartColNum -= 1;
 327         }
 328         else {
 329           die "Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column number doesn't exist in  $TextFile  \n";
 330         }
 331       }
 332     }
 333     else {
 334       $StartColNum = $TextFilesInfo{ColCount}[$Index] - 1;
 335     }
 336     # Set up columns lists for before and after the addition of calculated column values
 337     # for each text file...
 338     my($BeforeStartColNum, $AfterStartColNum, $FirstColNum, $LastColNum, $ColNum, $Part1StartColNum, $Part1EndColNum, $Part2StartColNum, $Part2EndColNum, @Part1ColNums, @Part2ColNums);
 339 
 340     $FirstColNum = 0; $LastColNum = $TextFilesInfo{ColCount}[$Index] - 1;
 341 
 342     $BeforeStartColNum = $StartColNum - 1;
 343     $AfterStartColNum = $StartColNum + 1;
 344 
 345     if ($OptionsInfo{StartColMode} =~ /^after$/i) {
 346       $Part1StartColNum = $FirstColNum; $Part1EndColNum = $StartColNum;
 347       $Part2StartColNum = $AfterStartColNum; $Part2EndColNum = $LastColNum;
 348     }
 349     else {
 350       $Part1StartColNum = $FirstColNum; $Part1EndColNum = $BeforeStartColNum;
 351       $Part2StartColNum = $StartColNum; $Part2EndColNum = $LastColNum;
 352     }
 353     @Part1ColNums = (); @Part2ColNums = ();
 354     for $ColNum (0 .. $TextFilesInfo{ColCount}[$Index]) {
 355       if ($ColNum >= $Part1StartColNum && $ColNum <= $Part1EndColNum) {
 356         push @Part1ColNums, $ColNum;
 357       }
 358     }
 359     for $ColNum (0 .. $TextFilesInfo{ColCount}[$Index]) {
 360       if ($ColNum >= $Part2StartColNum && $ColNum <= $Part2EndColNum) {
 361         push @Part2ColNums, $ColNum;
 362       }
 363     }
 364     push @{$TextFilesInfo{ColNumsBeforeNew}[$Index]}, @Part1ColNums;
 365     push @{$TextFilesInfo{ColNumsAfterNew}[$Index]}, @Part2ColNums;
 366 
 367     # Setup column labels for calculated values...
 368     for $Value (keys %NewValueLabels) {
 369       $Label = $NewValueLabels{$Value};
 370 
 371       # Make sure it doesn't already exists...
 372       $Count = 1;
 373       $NewLabel = $Label;
 374       while (exists $TextFilesInfo{ColLabelToNumMap}[$Index]{$NewLabel}) {
 375         $Count++;
 376         $NewLabel = $Label . $Count;
 377       }
 378       $TextFilesInfo{ValueLabelsMap}[$Index]{$Value} = $NewLabel;
 379     }
 380   }
 381 }
 382 
 383 # Retrieve information about input text files...
 384 sub RetrieveTextFilesInfo {
 385   my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, @ColLabels, $OutFileRoot,  $OutFile, $ColNum, $ColLabel);
 386 
 387   %TextFilesInfo = ();
 388 
 389   @{$TextFilesInfo{FileOkay}} = ();
 390   @{$TextFilesInfo{ColCount}} = ();
 391   @{$TextFilesInfo{ColLabels}} = ();
 392   @{$TextFilesInfo{ColLabelToNumMap}} = ();
 393   @{$TextFilesInfo{InDelim}} = ();
 394   @{$TextFilesInfo{OutFile}} = ();
 395 
 396   FILELIST: for $Index (0 .. $#TextFilesList) {
 397     $TextFile = $TextFilesList[$Index];
 398 
 399     $TextFilesInfo{FileOkay}[$Index] = 0;
 400     $TextFilesInfo{ColCount}[$Index] = 0;
 401     $TextFilesInfo{InDelim}[$Index] = "";
 402     $TextFilesInfo{OutFile}[$Index] = "";
 403 
 404     @{$TextFilesInfo{ColLabels}[$Index]} = ();
 405     %{$TextFilesInfo{ColLabelToNumMap}[$Index]} = ();
 406 
 407     if (!(-e $TextFile)) {
 408       warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
 409       next FILELIST;
 410     }
 411     if (!CheckFileType($TextFile, "csv tsv")) {
 412       warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
 413       next FILELIST;
 414     }
 415     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
 416     if ($FileExt =~ /^tsv$/i) {
 417       $InDelim = "\t";
 418     }
 419     else {
 420       $InDelim = "\,";
 421       if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
 422         warn "Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n";
 423         next FILELIST;
 424       }
 425       if ($Options{indelim} =~ /^semicolon$/i) {
 426         $InDelim = "\;";
 427       }
 428     }
 429 
 430     if (!open TEXTFILE, "$TextFile") {
 431       warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
 432       next FILELIST;
 433     }
 434 
 435     $Line = GetTextLine(\*TEXTFILE);
 436     @ColLabels = quotewords($InDelim, 0, $Line);
 437     close TEXTFILE;
 438 
 439     $FileDir = ""; $FileName = ""; $FileExt = "";
 440     ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
 441     $FileExt = "csv";
 442     if ($Options{outdelim} =~ /^tab$/i) {
 443       $FileExt = "tsv";
 444     }
 445     if ($Options{root} && (@TextFilesList == 1)) {
 446       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
 447       if ($RootFileName && $RootFileExt) {
 448         $FileName = $RootFileName;
 449       }
 450       else {
 451         $FileName = $Options{root};
 452       }
 453       $OutFileRoot = $FileName;
 454     }
 455     else {
 456       $OutFileRoot = $FileName . "ElementalAnalysis";
 457     }
 458 
 459     $OutFile = $OutFileRoot . ".$FileExt";
 460     if (lc($OutFile) eq lc($TextFile)) {
 461       warn "Warning: Ignoring file $TextFile:Output file name, $OutFile, is same as input text file name, $TextFile\n";
 462       next FILELIST;
 463     }
 464     if (!$Options{overwrite}) {
 465       if (-e $OutFile) {
 466         warn "Warning: Ignoring file $TextFile: The file $OutFile already exists\n";
 467         next FILELIST;
 468       }
 469     }
 470 
 471     $TextFilesInfo{FileOkay}[$Index] = 1;
 472     $TextFilesInfo{InDelim}[$Index] = $InDelim;
 473     $TextFilesInfo{OutFile}[$Index] = "$OutFile";
 474 
 475     $TextFilesInfo{ColCount}[$Index] = @ColLabels;
 476     push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
 477     for $ColNum (0 .. $#ColLabels) {
 478       $ColLabel = $ColLabels[$ColNum];
 479       $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel} = $ColNum;
 480     }
 481   }
 482 
 483 }
 484 
 485 # Process option values...
 486 sub ProcessOptions {
 487   %OptionsInfo = ();
 488 
 489   $OptionsInfo{Mode} = $Options{mode};
 490 
 491   $OptionsInfo{ColMode} = $Options{colmode};
 492   $OptionsInfo{StartColMode} = $Options{startcolmode};
 493 
 494   $OptionsInfo{Fast} = defined $Options{fast} ? $Options{fast} : undef;
 495 
 496   $OptionsInfo{DetailLevel} = $Options{detail};
 497   $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
 498   $OptionsInfo{Precision} = $Options{precision};
 499 
 500   $OptionsInfo{InDelim} = $Options{indelim};
 501 
 502   $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
 503   $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
 504 
 505   $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
 506   $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
 507 
 508   $OptionsInfo{StartCol} = defined $Options{startcol} ? $Options{startcol} : undef;
 509 
 510   $OptionsInfo{FormulaCol} = defined $Options{formulacol} ? $Options{formulacol} : undef;
 511   $OptionsInfo{SpecifiedFormulaCol} = "";
 512 
 513   if (defined $Options{formulacol}) {
 514     $OptionsInfo{SpecifiedFormulaCol} = $Options{formulacol};
 515     if ($Options{colmode} =~ /^colnum$/i) {
 516       if (!IsPositiveInteger($OptionsInfo{SpecifiedFormulaCol})) {
 517         die "Error: Invalid value $Options{formulacol} specified using \"-f -formulacol\" option: Allowed values: > 0\n";
 518       }
 519     }
 520   }
 521 
 522   # Setup what to calculate...
 523   @{$OptionsInfo{SpecifiedCalculations}} = ();
 524   if ($Options{mode} =~ /^All$/i) {
 525     @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
 526   }
 527   else {
 528     my($Mode, $ModeValue, @SpecifiedModeValues);
 529     $Mode = $Options{mode};
 530     $Mode =~ s/ //g;
 531     @SpecifiedModeValues = split /\,/, $Mode;
 532     for $ModeValue (@SpecifiedModeValues) {
 533       if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
 534         if ($ModeValue =~ /^All$/i) {
 535           die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
 536         }
 537         else {
 538           die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
 539         }
 540       }
 541       push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
 542     }
 543   }
 544 
 545   $OptionsInfo{ValueColLabels} = defined $Options{valuecollabels} ? $Options{valuecollabels} : undef;
 546   @{$OptionsInfo{SpecifiedValueLabels}} = ();
 547 
 548   if ($Options{valuecollabels}) {
 549     my($Value, $Label, @ValueLabels);
 550     @ValueLabels = split /\,/, $Options{valuecollabels};
 551     if (@ValueLabels % 2) {
 552       die "Error: The value specified, $Options{valuecollabels}, for option \"-v --valuecollabels\" is not valid: It must contain even number of comma delimited values\n";
 553     }
 554     my($Index);
 555     for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
 556       $Value = $ValueLabels[$Index];
 557       $Value =~ s/ //g;
 558       $Label = $ValueLabels[$Index + 1];
 559       if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
 560         die "Error: The value specified, $Value, using option \"-v --valuecollabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
 561       }
 562       push @{$OptionsInfo{SpecifiedValueLabels}}, ($Value, $Label);
 563     }
 564   }
 565 }
 566 
 567 # Setup script usage  and retrieve command line arguments specified using various options...
 568 sub SetupScriptUsage {
 569 
 570   # Retrieve all the options...
 571   %Options = ();
 572   $Options{colmode} = "colnum";
 573   $Options{detail} = 1;
 574   $Options{mode} = "All";
 575   $Options{indelim} = "comma";
 576   $Options{outdelim} = "comma";
 577   $Options{precision} = 2;
 578   $Options{quote} = "yes";
 579   $Options{startcolmode} = "after";
 580 
 581   if (!GetOptions(\%Options, "colmode|c=s", "detail|d=i", "fast", "formulacol|f=s", "help|h", "indelim=s", "mode|m=s", "outdelim=s", "overwrite|o", "precision|p=i", "quote|q=s", "root|r=s", "startcol|s=s", "startcolmode=s", "valuecollabels|v=s", "workingdir|w=s")) {
 582     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
 583   }
 584   if ($Options{workingdir}) {
 585     if (! -d $Options{workingdir}) {
 586       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
 587     }
 588     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
 589   }
 590   if ($Options{colmode} !~ /^(colnum|collabel)$/i) {
 591     die "Error: The value specified, $Options{colmode}, for option \"-c --colmode\" is not valid. Allowed values: colnum or collabel\n";
 592   }
 593   if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
 594     die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n";
 595   }
 596   if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
 597     die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
 598   }
 599   if (!IsPositiveInteger($Options{precision})) {
 600     die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
 601   }
 602   if ($Options{quote} !~ /^(yes|no)$/i) {
 603     die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
 604   }
 605   if ($Options{startcolmode} !~ /^(before|after)$/i) {
 606     die "Error: The value specified, $Options{quote}, for option \"--startcolmode\" is not valid. Allowed values: before or after\n";
 607   }
 608   if (!IsPositiveInteger($Options{detail})) {
 609     die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
 610   }
 611 }
 612