diff bin/ElementalAnalysisTextFiles.pl @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/ElementalAnalysisTextFiles.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,788 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: ElementalAnalysisTextFiles.pl,v $
+# $Date: 2015/02/28 20:46:19 $
+# $Revision: 1.28 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# Copyright (C) 2015 Manish Sud. All rights reserved.
+#
+# This file is part of MayaChemTools.
+#
+# MayaChemTools is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of fitness
+# for a particular purpose.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use FindBin; use lib "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use MolecularFormula;
+
+my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
+
+# Autoflush STDOUT
+$| = 1;
+
+# Starting message...
+$ScriptName = basename($0);
+print "\n$ScriptName: Starting...\n\n";
+$StartTime = new Benchmark;
+
+# Get the options and setup script...
+SetupScriptUsage();
+if ($Options{help} || @ARGV < 1) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+my(@TextFilesList);
+@TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
+
+# Process options...
+my(%OptionsInfo);
+print "Processing options...\n";
+ProcessOptions();
+
+print "Checking input text file(s)...\n";
+my(%TextFilesInfo);
+RetrieveTextFilesInfo();
+RetrieveColumnsAndLabelsInfo();
+
+# Generate output files...
+my($FileIndex);
+if (@TextFilesList > 1) {
+  print "\nProcessing text files...\n";
+}
+for $FileIndex (0 .. $#TextFilesList) {
+  if ($TextFilesInfo{FileOkay}[$FileIndex]) {
+    print "\nProcessing file $TextFilesList[$FileIndex]...\n";
+    PerformElementalAnalysis($FileIndex);
+  }
+}
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Perform elemental analysis...
+sub PerformElementalAnalysis {
+  my($Index) = @_;
+  my($TextFile, $NewTextFile, $FormulaCol, $Line, $NewLine, $FormulaColValue, $InDelim, $ColNum, $Value, $Status, $ErrorMsg, @ColLabels, @LineWords, @ColNumsBeforeNew, @ColNumsAfterNew);
+
+  $TextFile = $TextFilesList[$Index];
+  $InDelim = $TextFilesInfo{InDelim}[$Index];
+  $NewTextFile = $TextFilesInfo{OutFile}[$Index];
+  $FormulaCol = $TextFilesInfo{FormulaColNum}[$Index];
+
+  @ColNumsBeforeNew = @{$TextFilesInfo{ColNumsBeforeNew}[$Index]};
+  @ColNumsAfterNew = @{$TextFilesInfo{ColNumsAfterNew}[$Index]};
+
+  print "Generating new Text file $NewTextFile...\n";
+  open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n";
+  open TEXTFILE, "$TextFile" or die "Error: Can't open $TextFile: $! \n";
+
+  # Skip over column labels from old file...
+  $Line = GetTextLine(\*TEXTFILE);
+
+  # Add column lablels in new file...
+  @ColLabels = ();
+  for $ColNum (@ColNumsBeforeNew) {
+    push @ColLabels, $TextFilesInfo{ColLabels}[$Index][$ColNum];
+  }
+  for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
+    push @ColLabels, $TextFilesInfo{ValueLabelsMap}[$Index]{$Value};
+  }
+  for $ColNum (@ColNumsAfterNew) {
+    push @ColLabels, $TextFilesInfo{ColLabels}[$Index][$ColNum];
+  }
+  $NewLine = '';
+  $NewLine = JoinWords(\@ColLabels, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+  print NEWTEXTFILE "$NewLine\n";
+
+  # Go over all rows...
+  my($LineCount, $ElementsRef, $ElementCompositionRef, $CalculationType, $CalculatedValue, @CalculatedValues);
+
+  $LineCount = 1;
+  TEXTLINE: while ($Line = GetTextLine(\*TEXTFILE)) {
+    @LineWords = quotewords($InDelim, 0, $Line);
+    $LineCount++;
+
+    @CalculatedValues = ();
+    for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
+      push @CalculatedValues, '';
+    }
+    if ($FormulaCol > @LineWords) {
+      $ErrorMsg = "Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] not found";
+      PrintErrorMsg($Line, $ErrorMsg);
+      ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
+      next TEXTLINE;
+    }
+
+    # Make sure it's a valid molecular formula...
+    $FormulaColValue = $LineWords[$FormulaCol];
+    if ($OptionsInfo{CheckFormula}) {
+      ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($FormulaColValue);
+      if (!$Status) {
+	$ErrorMsg = "Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] value is not valid: $ErrorMsg";
+	PrintErrorMsg($Line, $ErrorMsg);
+	ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
+	next TEXTLINE;
+      }
+    }
+
+    # Calculate appropriate values and write 'em out...
+    @CalculatedValues = ();
+    for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
+      if ($CalculationType =~ /^ElementalAnalysis$/i) {
+	($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($FormulaColValue);
+	$CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
+      }
+      elsif ($CalculationType =~ /^MolecularWeight$/i) {
+	$CalculatedValue = MolecularFormula::CalculateMolecularWeight($FormulaColValue);
+	$CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
+      }
+      elsif ($CalculationType =~ /^ExactMass$/i) {
+	$CalculatedValue = MolecularFormula::CalculateExactMass($FormulaColValue);
+	$CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
+      }
+      else {
+	$CalculatedValue = '';
+      }
+      push @CalculatedValues, $CalculatedValue;
+    }
+
+    ComposeAndWriteNewLine(\*NEWTEXTFILE, \@LineWords, \@ColNumsBeforeNew, \@ColNumsAfterNew, \@CalculatedValues);
+  }
+  close NEWTEXTFILE;
+  close TEXTFILE;
+
+}
+
+# Write out new line using old and new calculated data...
+sub ComposeAndWriteNewLine {
+  my($NewTextFileRef, $OldLineWordsRef, $ColNumsBeforeNewRef, $ColNumsAfterNewRef, $CalculatedValuesRef) = @_;
+  my($NewLine, $ColNum, $Value, @NewLineWords);
+
+  @NewLineWords = ();
+  for $ColNum (@{$ColNumsBeforeNewRef}) {
+    push @NewLineWords, $OldLineWordsRef->[$ColNum];
+  }
+  for $Value (@{$CalculatedValuesRef}) {
+    push @NewLineWords, $Value;
+  }
+  for $ColNum (@{$ColNumsAfterNewRef}) {
+    push @NewLineWords, $OldLineWordsRef->[$ColNum];
+  }
+  $NewLine = JoinWords(\@NewLineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
+  print $NewTextFileRef "$NewLine\n";
+}
+
+# Print out error message...
+sub PrintErrorMsg {
+  my($Line, $ErrorMsg) = @_;
+
+  if ($OptionsInfo{DetailLevel} >= 2 ) {
+    print "$ErrorMsg: $Line\n";
+  }
+  elsif ($OptionsInfo{DetailLevel} >= 1) {
+    print "$ErrorMsg\n";
+  }
+}
+
+# Process formula columns and other information...
+sub RetrieveColumnsAndLabelsInfo {
+  RetrieveFormulaColumnsInfo();
+  RetrieveStartColumnsAndValueLabelsInfo();
+}
+
+# Make sure specified formula column are okay...
+sub RetrieveFormulaColumnsInfo {
+  my($Index, $TextFile);
+
+  @{$TextFilesInfo{FormulaColNum}} = ();
+
+ FILELIST: for $Index (0 .. $#TextFilesList) {
+    $TextFile = $TextFilesList[$Index];
+
+    $TextFilesInfo{FormulaColNum}[$Index] = 0;
+
+    if ($TextFilesInfo{FileOkay}[$Index]) {
+      my($FormulaColNum, $FormulaColValid);
+
+      $FormulaColNum = 0;
+      $FormulaColValid = 0;
+      if ($OptionsInfo{SpecifiedFormulaCol}) {
+	if ($OptionsInfo{ColMode} =~ /^colnum$/i) {
+	  if ($OptionsInfo{SpecifiedFormulaCol} <= $TextFilesInfo{ColCount}[$Index]) {
+	    $FormulaColNum = $OptionsInfo{SpecifiedFormulaCol} - 1;
+	    $FormulaColValid = 1;
+	  }
+	}
+	else {
+	  if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$OptionsInfo{SpecifiedFormulaCol}})) {
+	    $FormulaColNum =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$OptionsInfo{SpecifiedFormulaCol}};
+	    $FormulaColValid = 1;
+	  }
+	}
+      }
+      else {
+	# Grab the first column with the word Formula in its label...
+	my($ColLabel);
+	LABEL: for $ColLabel (@{$TextFilesInfo{ColLabels}[$Index]}) {
+	  if ($ColLabel =~ /Formula/i) {
+	    $FormulaColNum =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel};
+	    $FormulaColValid = 1;
+	    last LABEL;
+	  }
+	}
+      }
+      if ($FormulaColValid) {
+	$TextFilesInfo{FormulaColNum}[$Index] = $FormulaColNum;
+      }
+      else {
+	if ($OptionsInfo{SpecifiedFormulaCol}) {
+	  warn "Warning: Ignoring file $TextFile: Formula column specified, $OptionsInfo{SpecifiedFormulaCol}, using \"f --formulacol\" option doesn't exist\n";
+	}
+	else {
+	  warn "Warning: Ignoring file $TextFile: Column label containing the word Formula doesn't exist\n";
+	}
+	$TextFilesInfo{FileOkay}[$Index] = 0;
+      }
+    }
+  }
+}
+
+# Setup starting column number for adding calculated values and
+# column lables to use for these values...
+sub RetrieveStartColumnsAndValueLabelsInfo {
+  my($Index, $TextFile, $SpecifiedStartColNum, $StartColNum, $Label, $Value, $NewLabel, $Count, $BeforeStartColNum, $AfterStartColNum, $FirstColNum, $LastColNum, $ColNum, $Part1StartColNum, $Part1EndColNum, $Part2StartColNum, $Part2EndColNum, @Part1ColNums, @Part2ColNums);
+
+  # Start column number for inserting new values...
+  $SpecifiedStartColNum = "last";
+  if (defined($OptionsInfo{StartCol})) {
+    if (length($OptionsInfo{StartCol})) {
+      $SpecifiedStartColNum = $OptionsInfo{StartCol}
+    }
+  }
+
+  # Column labels for for new calculated values...
+  my(%NewValueLabels) = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass');
+  if (@{$OptionsInfo{SpecifiedValueLabels}}) {
+    for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueLabels}}; $Index +=2) {
+      $Value = $OptionsInfo{SpecifiedValueLabels}[$Index];
+      $Label = $OptionsInfo{SpecifiedValueLabels}[$Index + 1];
+      if (exists $NewValueLabels{$Value}) {
+	$NewValueLabels{$Value} = $Label;
+      }
+    }
+  }
+
+  @{$TextFilesInfo{ColNumsBeforeNew}} = ();
+  @{$TextFilesInfo{ColNumsAfterNew}} = ();
+  @{$TextFilesInfo{ValueLabelsMap}} = ();
+
+  FILELIST: for $Index (0 .. $#TextFilesList) {
+    $TextFile = $TextFilesList[$Index];
+
+    @{$TextFilesInfo{ColNumsBeforeNew}[$Index]} = ();
+    @{$TextFilesInfo{ColNumsAfterNew}[$Index]} = ();
+    %{$TextFilesInfo{ValueLabelsMap}[$Index]} = ();
+
+    if (!$TextFilesInfo{FileOkay}[$Index]) {
+      next FILELIST;
+    }
+
+    if ($SpecifiedStartColNum !~ /^last$/i) {
+      if ($OptionsInfo{ColMode} =~ /^collabel$/i) {
+	if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedStartColNum})) {
+	  $StartColNum = $TextFilesInfo{ColLabelToNumMap}[$Index]{$SpecifiedStartColNum};
+	}
+	else {
+	  die "Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column name doesn't exist in  $TextFile  \n";
+	}
+      }
+      else {
+	if ($SpecifiedStartColNum > 0 && $SpecifiedStartColNum <= $TextFilesInfo{ColCount}[$Index]) {
+	  $StartColNum -= 1;
+	}
+	else {
+	  die "Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column number doesn't exist in  $TextFile  \n";
+	}
+      }
+    }
+    else {
+      $StartColNum = $TextFilesInfo{ColCount}[$Index] - 1;
+    }
+    # Set up columns lists for before and after the addition of calculated column values
+    # for each text file...
+    my($BeforeStartColNum, $AfterStartColNum, $FirstColNum, $LastColNum, $ColNum, $Part1StartColNum, $Part1EndColNum, $Part2StartColNum, $Part2EndColNum, @Part1ColNums, @Part2ColNums);
+
+    $FirstColNum = 0; $LastColNum = $TextFilesInfo{ColCount}[$Index] - 1;
+
+    $BeforeStartColNum = $StartColNum - 1;
+    $AfterStartColNum = $StartColNum + 1;
+
+    if ($OptionsInfo{StartColMode} =~ /^after$/i) {
+      $Part1StartColNum = $FirstColNum; $Part1EndColNum = $StartColNum;
+      $Part2StartColNum = $AfterStartColNum; $Part2EndColNum = $LastColNum;
+    }
+    else {
+      $Part1StartColNum = $FirstColNum; $Part1EndColNum = $BeforeStartColNum;
+      $Part2StartColNum = $StartColNum; $Part2EndColNum = $LastColNum;
+    }
+    @Part1ColNums = (); @Part2ColNums = ();
+    for $ColNum (0 .. $TextFilesInfo{ColCount}[$Index]) {
+      if ($ColNum >= $Part1StartColNum && $ColNum <= $Part1EndColNum) {
+	push @Part1ColNums, $ColNum;
+      }
+    }
+    for $ColNum (0 .. $TextFilesInfo{ColCount}[$Index]) {
+      if ($ColNum >= $Part2StartColNum && $ColNum <= $Part2EndColNum) {
+	push @Part2ColNums, $ColNum;
+      }
+    }
+    push @{$TextFilesInfo{ColNumsBeforeNew}[$Index]}, @Part1ColNums;
+    push @{$TextFilesInfo{ColNumsAfterNew}[$Index]}, @Part2ColNums;
+
+    # Setup column labels for calculated values...
+    for $Value (keys %NewValueLabels) {
+      $Label = $NewValueLabels{$Value};
+
+      # Make sure it doesn't already exists...
+      $Count = 1;
+      $NewLabel = $Label;
+      while (exists $TextFilesInfo{ColLabelToNumMap}[$Index]{$NewLabel}) {
+	$Count++;
+	$NewLabel = $Label . $Count;
+      }
+      $TextFilesInfo{ValueLabelsMap}[$Index]{$Value} = $NewLabel;
+    }
+  }
+}
+
+# Retrieve information about input text files...
+sub RetrieveTextFilesInfo {
+  my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, @ColLabels, $OutFileRoot,  $OutFile, $ColNum, $ColLabel);
+
+  %TextFilesInfo = ();
+
+  @{$TextFilesInfo{FileOkay}} = ();
+  @{$TextFilesInfo{ColCount}} = ();
+  @{$TextFilesInfo{ColLabels}} = ();
+  @{$TextFilesInfo{ColLabelToNumMap}} = ();
+  @{$TextFilesInfo{InDelim}} = ();
+  @{$TextFilesInfo{OutFile}} = ();
+
+  FILELIST: for $Index (0 .. $#TextFilesList) {
+    $TextFile = $TextFilesList[$Index];
+
+    $TextFilesInfo{FileOkay}[$Index] = 0;
+    $TextFilesInfo{ColCount}[$Index] = 0;
+    $TextFilesInfo{InDelim}[$Index] = "";
+    $TextFilesInfo{OutFile}[$Index] = "";
+
+    @{$TextFilesInfo{ColLabels}[$Index]} = ();
+    %{$TextFilesInfo{ColLabelToNumMap}[$Index]} = ();
+
+    if (!(-e $TextFile)) {
+      warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
+      next FILELIST;
+    }
+    if (!CheckFileType($TextFile, "csv tsv")) {
+      warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
+      next FILELIST;
+    }
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
+    if ($FileExt =~ /^tsv$/i) {
+      $InDelim = "\t";
+    }
+    else {
+      $InDelim = "\,";
+      if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
+	warn "Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n";
+	next FILELIST;
+      }
+      if ($Options{indelim} =~ /^semicolon$/i) {
+	$InDelim = "\;";
+      }
+    }
+
+    if (!open TEXTFILE, "$TextFile") {
+      warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+
+    $Line = GetTextLine(\*TEXTFILE);
+    @ColLabels = quotewords($InDelim, 0, $Line);
+    close TEXTFILE;
+
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
+    $FileExt = "csv";
+    if ($Options{outdelim} =~ /^tab$/i) {
+      $FileExt = "tsv";
+    }
+    if ($Options{root} && (@TextFilesList == 1)) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+      if ($RootFileName && $RootFileExt) {
+	$FileName = $RootFileName;
+      }
+      else {
+	$FileName = $Options{root};
+      }
+      $OutFileRoot = $FileName;
+    }
+    else {
+      $OutFileRoot = $FileName . "ElementalAnalysis";
+    }
+
+    $OutFile = $OutFileRoot . ".$FileExt";
+    if (lc($OutFile) eq lc($TextFile)) {
+      warn "Warning: Ignoring file $TextFile:Output file name, $OutFile, is same as input text file name, $TextFile\n";
+      next FILELIST;
+    }
+    if (!$Options{overwrite}) {
+      if (-e $OutFile) {
+	warn "Warning: Ignoring file $TextFile: The file $OutFile already exists\n";
+	next FILELIST;
+      }
+    }
+
+    $TextFilesInfo{FileOkay}[$Index] = 1;
+    $TextFilesInfo{InDelim}[$Index] = $InDelim;
+    $TextFilesInfo{OutFile}[$Index] = "$OutFile";
+
+    $TextFilesInfo{ColCount}[$Index] = @ColLabels;
+    push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
+    for $ColNum (0 .. $#ColLabels) {
+      $ColLabel = $ColLabels[$ColNum];
+      $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel} = $ColNum;
+    }
+  }
+
+}
+
+# Process option values...
+sub ProcessOptions {
+  %OptionsInfo = ();
+
+  $OptionsInfo{Mode} = $Options{mode};
+
+  $OptionsInfo{ColMode} = $Options{colmode};
+  $OptionsInfo{StartColMode} = $Options{startcolmode};
+
+  $OptionsInfo{Fast} = defined $Options{fast} ? $Options{fast} : undef;
+
+  $OptionsInfo{DetailLevel} = $Options{detail};
+  $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
+  $OptionsInfo{Precision} = $Options{precision};
+
+  $OptionsInfo{InDelim} = $Options{indelim};
+
+  $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
+  $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
+
+  $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
+  $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
+
+  $OptionsInfo{StartCol} = defined $Options{startcol} ? $Options{startcol} : undef;
+
+  $OptionsInfo{FormulaCol} = defined $Options{formulacol} ? $Options{formulacol} : undef;
+  $OptionsInfo{SpecifiedFormulaCol} = "";
+
+  if (defined $Options{formulacol}) {
+    $OptionsInfo{SpecifiedFormulaCol} = $Options{formulacol};
+    if ($Options{colmode} =~ /^colnum$/i) {
+      if (!IsPositiveInteger($OptionsInfo{SpecifiedFormulaCol})) {
+	die "Error: Invalid value $Options{formulacol} specified using \"-f -formulacol\" option: Allowed values: > 0\n";
+      }
+    }
+  }
+
+  # Setup what to calculate...
+  @{$OptionsInfo{SpecifiedCalculations}} = ();
+  if ($Options{mode} =~ /^All$/i) {
+    @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
+  }
+  else {
+    my($Mode, $ModeValue, @SpecifiedModeValues);
+    $Mode = $Options{mode};
+    $Mode =~ s/ //g;
+    @SpecifiedModeValues = split /\,/, $Mode;
+    for $ModeValue (@SpecifiedModeValues) {
+      if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
+	if ($ModeValue =~ /^All$/i) {
+	  die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
+	}
+	else {
+	  die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
+	}
+      }
+      push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
+    }
+  }
+
+  $OptionsInfo{ValueColLabels} = defined $Options{valuecollabels} ? $Options{valuecollabels} : undef;
+  @{$OptionsInfo{SpecifiedValueLabels}} = ();
+
+  if ($Options{valuecollabels}) {
+    my($Value, $Label, @ValueLabels);
+    @ValueLabels = split /\,/, $Options{valuecollabels};
+    if (@ValueLabels % 2) {
+      die "Error: The value specified, $Options{valuecollabels}, for option \"-v --valuecollabels\" is not valid: It must contain even number of comma delimited values\n";
+    }
+    my($Index);
+    for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
+      $Value = $ValueLabels[$Index];
+      $Value =~ s/ //g;
+      $Label = $ValueLabels[$Index + 1];
+      if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
+	die "Error: The value specified, $Value, using option \"-v --valuecollabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
+      }
+      push @{$OptionsInfo{SpecifiedValueLabels}}, ($Value, $Label);
+    }
+  }
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{colmode} = "colnum";
+  $Options{detail} = 1;
+  $Options{mode} = "All";
+  $Options{indelim} = "comma";
+  $Options{outdelim} = "comma";
+  $Options{precision} = 2;
+  $Options{quote} = "yes";
+  $Options{startcolmode} = "after";
+
+  if (!GetOptions(\%Options, "colmode|c=s", "detail|d=i", "fast", "formulacol|f=s", "help|h", "indelim=s", "mode|m=s", "outdelim=s", "overwrite|o", "precision|p=i", "quote|q=s", "root|r=s", "startcol|s=s", "startcolmode=s", "valuecollabels|v=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
+  }
+  if ($Options{workingdir}) {
+    if (! -d $Options{workingdir}) {
+      die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
+    }
+    chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
+  }
+  if ($Options{colmode} !~ /^(colnum|collabel)$/i) {
+    die "Error: The value specified, $Options{colmode}, for option \"-c --colmode\" is not valid. Allowed values: colnum or collabel\n";
+  }
+  if ($Options{indelim} !~ /^(comma|semicolon)$/i) {
+    die "Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n";
+  }
+  if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
+    die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
+  }
+  if (!IsPositiveInteger($Options{precision})) {
+    die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
+  }
+  if ($Options{quote} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
+  }
+  if ($Options{startcolmode} !~ /^(before|after)$/i) {
+    die "Error: The value specified, $Options{quote}, for option \"--startcolmode\" is not valid. Allowed values: before or after\n";
+  }
+  if (!IsPositiveInteger($Options{detail})) {
+    die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+ElementalAnalysisTextFiles.pl - Perform elemental analysis using formula column in TextFile(s)
+
+=head1 SYNOPSIS
+
+ElementalAnalysisTextFiles.pl TextFile(s)...
+
+ElementalAnalysisTextFiles.pl [B<-c, --colmode> colnum | collabel] [B<-d, --detail> infolevel] [B<-f, --fast>]
+[B<-f, --formulacol> colnum | collabel] [B<-h, --help>] [B<--indelim> comma | semicolon]
+[B<-m, --mode> All | "ElementalAnysis, [MolecularWeight, ExactMass]"] [B<-o, --overwrite>]
+[B<--outdelim> comma | tab | semicolon] [B<-p, --precision> number] [B<-q, --quote> yes | no]
+[B<-r, --root> rootname] [B<-s, --startcol> colnum | collabel] [B<--startcolmode> before | after]
+B<-v --valuecollabels> [Name, Label, [Name, Label,...]] [B<-w, --workingdir> dirname] TextFile(s)...
+
+=head1 DESCRIPTION
+
+Perform elemental analysis using molecular formula column specified by a column number or label in
+I<TextFile(s)>.
+
+In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
+other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
+8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
+D and T, are not supported.
+
+The valid file extensions are I<.csv> and I<.tsv> for comma/semicolon and tab delimited
+text files respectively. All other file names are ignored. All the text files in a
+current directory can be specified by I<*.csv>, I<*.tsv>, or the current directory
+name. The B<--indelim> option determines the format of I<TextFile(s)>. Any file
+which doesn't correspond to the format indicated by B<--indelim> option is ignored.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-c, --colmode> I<colnum | collabel>
+
+Specify how columns are identified in I<TextFile(s)>: using column number or column
+label. Possible values: I<colnum or collabel>. Default value: I<colnum>.
+
+=item B<-d, --detail> I<infolevel>
+
+Level of information to print about lines being ignored. Default: I<1>. Possible values:
+I<1, 2 or 3>.
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<--fast>
+
+In this mode, the formula column specified using B<-f, --formulacol> option is assumed
+to contain valid molecular formula data and initial formula validation check is skipped.
+
+=item B<-f, --formulacol> I<col number | col name>
+
+This value is mode specific. It specifies molecular formula column to use for performing
+elemental analysis on I<TextFile(s)>. Possible values: I<col number or col label>.
+Default value: I<first column containing the word formula in its column label>.
+
+=item B<-m, --mode> I<All | "ElementalAnalysis,[MolecularWeight,ExactMass]">
+
+Specify what values to calculate using molecular formula in I<TextFile(s)>: calculate all supported
+values or specify a comma delimited list of values. Possible values: I<All | "ElementalAnalysis,
+[MolecularWeight, ExactMass]">. Default: I<All>
+
+=item B<--indelim> I<comma | semicolon>
+
+Input delimiter for CSV I<TextFile(s)>. Possible values: I<comma or semicolon>.
+Default value: I<comma>. For TSV files, this option is ignored and I<tab> is used as a
+delimiter.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<--outdelim> I<comma | tab | semicolon>
+
+Output text file delimiter. Possible values: I<comma, tab, or semicolon>
+Default value: I<comma>.
+
+=item B<-p, --precision> I<number>
+
+Precision of calculated values in the output file. Default: up to I<2> decimal places.
+Valid values: positive integers.
+
+=item B<-q, --quote> I<yes | no>
+
+Put quotes around column values in output text file. Possible values: I<yes or
+no>. Default value: I<yes>.
+
+=item B<-r, --root> I<rootname>
+
+New text file name is generated using the root: <Root>.<Ext>. Default new file
+name: <InitialTextFileName>ElementalAnalysis.<Ext>. The csv, and tsv
+<Ext> values are used for comma/semicolon, and tab delimited text files
+respectively. This option is ignored for multiple input files.
+
+=item B<-s, --startcol> I<colnum | collabel>
+
+This value is mode specific. It specifies the column in text files which is
+used for start adding calculated column values. For I<colnum> mode, specify
+column number and for I<collabel> mode, specify column label.
+
+Default value: I<last>. Start merge after the last column.
+
+=item B<--startcolmode> I<before | after>
+
+Start adding calculated column values after the B<-s, --startcol> value. Possible values: I<before or after>.
+Default value: I<after>.
+
+=item B<-v --valuecollabels> I<Name,Label,[Name,Label,...]>
+
+Specify column labels to use for calculated values. In general, it's a comma delimited
+list of value name and column label pairs. Supported value names: I<ElementalAnalysis,
+MolecularWeight,  and ExactMass>. Default labels: I<ElementalAnalysis, MolecularWeight,
+and ExactMass>.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To perform elemental analysis, calculate molecular weight and exact mass using formulas
+in a column with the word Formula in its column label and generate a new CSV text
+file NewSample1.csv, type:
+
+    % ElementalAnalysisTextFiles.pl -o -r NewSample1 Sample1.csv
+
+To perform elemental analysis using formulas in column number two, use column label
+Analysis for calculated data, and generate a new CSV text file NewSample1.csv, type:
+
+    % ElementalAnalysisTextFiles.pl --m ElementalAnalysis --formulacol 2
+      --valuecollabels "ElementalAnalysis,Analysis" -o -r NewSample1
+      Sample1.csv
+
+To calculate molecular weight using formula in column label Formula with four decimal
+precision and generate a new CSV text file NewSample1.csv, type
+
+    % ElementalAnalysisTextFiles.pl --m MolecularWeight --colmode collabel
+      --formulacol Formula --precision 4 -o -r NewSample1 Sample1.csv
+
+To calculate exact mass  using formula in column label Formula with four decimal
+precision, adding column for exact mass right after Formula column, and generate a
+new CSV text file NewSample1.csv, type
+
+    % ElementalAnalysisTextFiles.pl --m ExactMass --colmode collabel
+      --formulacol Formula --precision 4 --startcolmode after
+      --startcol Formula -o -r NewSample1 Sample1.csv
+
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+AnalyzeTextFilesData.pl, InfoTextFiles.pl, ExtractFromTextFiles.pl
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 Manish Sud. All rights reserved.
+
+This file is part of MayaChemTools.
+
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.
+
+=cut