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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/MergeTextFilesWithSD.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,718 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: MergeTextFilesWithSD.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $Revision: 1.39 $
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileHandle;
+use SDFileUtil;
+use FileUtil;
+use TextUtil;
+
+my($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($SDFile, @TextFilesList);
+@TextFilesList = ExpandFileNames(\@ARGV, "csv tsv");
+
+if (@TextFilesList < 2) {
+  die "Error: Specify one or more text files.\n";
+}
+$SDFile = shift @TextFilesList;
+
+# Process options...
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+# Setup information about input files...
+print "Checking input SD and text files...\n";
+my(%TextFilesInfo);
+ProcessSDFileInfo();
+RetrieveTextFilesInfo();
+RetrieveColumnsAndKeysInfo();
+
+# Merge files...
+print "\nGenerating new SD file $OptionsInfo{NewSDFile}...\n";
+MergeTextFilesWithSD();
+
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Merge all valid Text files with SD file...
+sub MergeTextFilesWithSD {
+  my($Index, $Line);
+
+  open NEWSDFILE, ">$OptionsInfo{NewSDFile}" or die "Error: Couldn't open $OptionsInfo{NewSDFile}: $! \n";
+
+  open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
+
+  @{$TextFilesInfo{FileHandle}} = ();
+  for $Index (0 .. $#TextFilesList) {
+    $TextFilesInfo{FileHandle}[$Index] = new FileHandle;
+
+    open $TextFilesInfo{FileHandle}[$Index], "$TextFilesList[$Index]" or die "Error: Couldn't open $TextFilesList[$Index]: $! \n";
+    GetTextLine($TextFilesInfo{FileHandle}[$Index]);
+  }
+
+  if ($OptionsInfo{Keys}) {
+    MergeTextColumnValuesUsingKeys(\*NEWSDFILE, \*SDFILE);
+  }
+  else {
+    MergeTextColumnValues(\*NEWSDFILE, \*SDFILE);
+  }
+
+  # Close all opened files...
+  close NEWSDFILE;
+  close SDFILE;
+  for $Index (0 .. $#TextFilesList) {
+    close $TextFilesInfo{FileHandle}[$Index];
+  }
+}
+
+# Merge the specified text columns into SD file...
+sub MergeTextColumnValues {
+  my($NewSDFileRef, $SDFileRef) = @_;
+  my($Index, $Value, $CmpdString, $Line, $InDelim, $ColNum, $ColIndex, @ColLabels, @ColValues, @LineWords);
+
+  while ($CmpdString = ReadCmpdString($SDFileRef)) {
+    $CmpdString =~ s/\$\$\$\$$//g;
+    print $NewSDFileRef "$CmpdString";
+
+    # Merge coulmn values from other text files...
+    @ColLabels = (); @ColValues = ();
+    for $Index (0 .. $#TextFilesList) {
+      push @ColLabels, @{$TextFilesInfo{ColToMergeLabels}[$Index]};
+      $InDelim = $TextFilesInfo{InDelim}[$Index];
+
+      if ($Line = GetTextLine($TextFilesInfo{FileHandle}[$Index])) {
+	@LineWords = quotewords($InDelim, 0, $Line);
+
+	for $ColNum (@{$TextFilesInfo{ColToMerge}[$Index]}) {
+	  $Value = ($ColNum < @LineWords) ? $LineWords[$ColNum] : "";
+	  push @ColValues, $Value;
+	}
+      }
+    }
+
+    for $ColIndex (0 .. $#ColLabels) {
+      print $NewSDFileRef "> <$ColLabels[$ColIndex]>\n$ColValues[$ColIndex]\n\n";
+    }
+    print $NewSDFileRef "\$\$\$\$\n";
+  }
+}
+
+# Merge the specified text columns into SD file using keys...
+sub MergeTextColumnValuesUsingKeys {
+  my($NewSDFileRef, $SDFileRef) = @_;
+  my($Index, $CmpdString, $Value, $InDelim, $KeyColNum, $KeyColValue, $Line, $ColIndex, $ColNum, @ColLabels, @ColValues, @LineWords, @CmpdLines, @TextFilesKeysToLinesMap, %DataFieldValues);
+
+  # Retrieve text lines from all the text files...
+  @TextFilesKeysToLinesMap = ();
+
+  for $Index (0 .. $#TextFilesList) {
+    $InDelim = $TextFilesInfo{InDelim}[$Index];
+    %{$TextFilesKeysToLinesMap[$Index]} = ();
+    $KeyColNum = $TextFilesInfo{KeysToUse}[$Index];
+
+    while ($Line = GetTextLine($TextFilesInfo{FileHandle}[$Index])) {
+      @LineWords = quotewords($InDelim, 0, $Line);
+
+      if ($KeyColNum < @LineWords) {
+	$KeyColValue = $LineWords[$KeyColNum];
+
+	if (length($KeyColValue)) {
+	  if (exists($TextFilesKeysToLinesMap[$Index]{$KeyColValue})) {
+	    warn "Warning: Ignoring line, $Line, in text file $TextFilesList[$Index]: Column key value, $KeyColValue, already exists\n";
+	  }
+	  else {
+	    @{$TextFilesKeysToLinesMap[$Index]{$KeyColValue}} = ();
+	    push @{$TextFilesKeysToLinesMap[$Index]{$KeyColValue}}, @LineWords;
+	  }
+	}
+      }
+    }
+  }
+
+  while ($CmpdString = ReadCmpdString($SDFileRef)) {
+    @CmpdLines = split "\n", $CmpdString;
+    %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+
+    if (exists($DataFieldValues{$OptionsInfo{SDKey}})) {
+      @ColLabels = (); @ColValues = ();
+      $CmpdString =~ s/\$\$\$\$$//g;
+      print $NewSDFileRef "$CmpdString";
+
+      $KeyColValue = $DataFieldValues{$OptionsInfo{SDKey}};
+
+      # Merge coulmn values from other text files...
+      for $Index (0 .. $#TextFilesList) {
+	push @ColLabels, @{$TextFilesInfo{ColToMergeLabels}[$Index]};
+	@LineWords = ();
+
+	if (exists($TextFilesKeysToLinesMap[$Index]{$KeyColValue})) {
+	  push @LineWords, @{$TextFilesKeysToLinesMap[$Index]{$KeyColValue}};
+	}
+
+	for $ColNum (@{$TextFilesInfo{ColToMerge}[$Index]}) {
+	  $Value = ($ColNum < @LineWords) ? $LineWords[$ColNum] : "";
+	  push @ColValues, $Value;
+	}
+      }
+
+      for $ColIndex (0 .. $#ColLabels) {
+	$Value = (($ColIndex < @ColValues) && IsNotEmpty($ColValues[$ColIndex]) ) ? $ColValues[$ColIndex] : "";
+	print $NewSDFileRef "> <$ColLabels[$ColIndex]>\n$Value\n\n";
+      }
+      print $NewSDFileRef "\$\$\$\$\n";
+    }
+  }
+}
+
+# Retrieve text file columns and keys information for specified options...
+sub RetrieveColumnsAndKeysInfo {
+  ProcessColumnsInfo();
+
+  if ($OptionsInfo{Keys}) {
+    ProcessKeysInfo();
+  }
+}
+
+# Process specified columns...
+sub ProcessColumnsInfo {
+  my($Index, $Values, $ColIndex, $ColNum, $ColLabel, @Words);
+
+  @{$TextFilesInfo{ColSpecified}} = ();
+  @{$TextFilesInfo{ColToMerge}} = ();
+  @{$TextFilesInfo{ColToMergeLabels}} = ();
+  @{$TextFilesInfo{ColToMergeNumToLabelMap}} = ();
+
+  for $Index (0 .. $#TextFilesList) {
+
+    @{$TextFilesInfo{ColSpecified}[$Index]} = ();
+
+    $Values = "all";
+    if ($OptionsInfo{Columns}) {
+      $Values = $OptionsInfo{ColValues}[$Index];
+    }
+
+    if ($Values =~ /all/i) {
+      if ($OptionsInfo{Mode} =~ /^colnum$/i) {
+	for $ColNum (1 .. $TextFilesInfo{ColCount}[$Index]) {
+	  push @{$TextFilesInfo{ColSpecified}[$Index]}, $ColNum;
+	}
+      } else {
+	push @{$TextFilesInfo{ColSpecified}[$Index]}, @{$TextFilesInfo{ColLabels}[$Index]};
+      }
+    }
+    else {
+      @Words = split ",", $Values;
+      push @{$TextFilesInfo{ColSpecified}[$Index]}, @Words;
+    }
+
+    @{$TextFilesInfo{ColToMerge}[$Index]} = ();
+    %{$TextFilesInfo{ColToMergeNumToLabelMap}[$Index]} = ();
+
+    if ($OptionsInfo{Mode} =~ /^collabel$/i) {
+      for $ColIndex (0 .. $#{$TextFilesInfo{ColSpecified}[$Index]}) {
+	$ColLabel = $TextFilesInfo{ColSpecified}[$Index][$ColIndex];
+
+	if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel})) {
+	  $ColNum = $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel};
+	  push @{$TextFilesInfo{ColToMerge}[$Index]}, $ColNum;
+	  $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum} = $ColLabel;
+	}
+	else {
+	  warn "Warning: Ignoring value, $ColLabel, specified using \"-c --column\" option: column name doesn't exist in  $TextFilesList[$Index]  \n";
+	}
+      }
+    }
+    else {
+      for $ColIndex (0 .. $#{$TextFilesInfo{ColSpecified}[$Index]}) {
+	$ColNum = $TextFilesInfo{ColSpecified}[$Index][$ColIndex];
+
+	# Make sure it's a numeric value...
+	if (!IsPositiveInteger($ColNum)) {
+	  warn "Warning: Ignoring value, $ColNum, specified using \"-c --column\" option:  Allowed integer values: > 0\n";
+	}
+	else {
+	  if ($ColNum > 0 && $ColNum <= $TextFilesInfo{ColCount}[$Index]) {
+	    $ColNum -= 1;
+	    push @{$TextFilesInfo{ColToMerge}[$Index]}, $ColNum;
+	    $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum} = $TextFilesInfo{ColLabels}[$Index][$ColNum];
+	  }
+	  else {
+	    warn "Warning: Ignoring value, $ColNum, specified using \"-c --column\" option: column number doesn't exist in  $TextFilesList[$Index]  \n";
+	  }
+	}
+      }
+    }
+
+    my (@TextFilesColToMergeSorted) = sort { $a <=> $b } @{$TextFilesInfo{ColToMerge}[$Index]};
+
+    @{$TextFilesInfo{ColToMerge}[$Index]} = ();
+    push @{$TextFilesInfo{ColToMerge}[$Index]}, @TextFilesColToMergeSorted;
+
+    # Set up the labels...
+    @{$TextFilesInfo{ColToMergeLabels}[$Index]} = ();
+    for $ColNum (@TextFilesColToMergeSorted) {
+      push @{$TextFilesInfo{ColToMergeLabels}[$Index]}, $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum};
+    }
+  }
+}
+
+# Process specified keys....
+sub ProcessKeysInfo {
+  my($Index, $ColNum, $ColLabel, $Key);
+
+  @{$TextFilesInfo{KeysSpecified}} = ();
+  @{$TextFilesInfo{KeysToUse}} = ();
+
+  for $Index (0 .. $#TextFilesList) {
+    $Key = $OptionsInfo{KeyValues}[$Index];
+
+    $TextFilesInfo{KeysSpecified}[$Index] = $Key;
+    $TextFilesInfo{KeysToUse}[$Index] = -1;
+
+    if ($OptionsInfo{Mode} =~ /^collabel$/i) {
+      $ColLabel = $Key;
+
+      if (exists($TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel})) {
+	$TextFilesInfo{KeysToUse}[$Index] =  $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel};
+      }
+      else {
+	warn "Warning: Ignoring value, $ColLabel, specified using \"-k --keys\" option: column name doesn't exist in  $TextFilesList[$Index]  \n";
+      }
+    }
+    else {
+      $ColNum = $Key;
+      if (!IsPositiveInteger($ColNum)) {
+	warn "Warning: Ignoring value, $ColNum, specified using \"-k --keys\" option: Allowed integer values: > 0  \n";
+      }
+      else {
+	if ($ColNum > 0 && $ColNum <= $TextFilesInfo{ColCount}[$Index]) {
+	  $TextFilesInfo{KeysToUse}[$Index] = $ColNum - 1;
+	}
+	else {
+	  warn "Warning: Ignoring value, $ColNum, specified using \"-k --keys\" option: column number doesn't exist in  $TextFilesList[$Index]  \n";
+	}
+      }
+    }
+  }
+
+  # Modify columns to merge list to make sure the columns identified by key are taken off the list
+  my(@TextFilesColToMergeFiltered, @TextFilesColToMergeLabelsFiltered);
+
+  for $Index (0 .. $#TextFilesList) {
+    @TextFilesColToMergeFiltered = ();
+    @TextFilesColToMergeLabelsFiltered = ();
+
+    for $ColNum (@{$TextFilesInfo{ColToMerge}[$Index]}) {
+      if ($TextFilesInfo{KeysToUse}[$Index] != $ColNum) {
+	push @TextFilesColToMergeFiltered, $ColNum;
+	push @TextFilesColToMergeLabelsFiltered, $TextFilesInfo{ColToMergeNumToLabelMap}[$Index]{$ColNum};
+      }
+    }
+
+    @{$TextFilesInfo{ColToMerge}[$Index]} = ();
+    push @{$TextFilesInfo{ColToMerge}[$Index]}, @TextFilesColToMergeFiltered;
+
+    @{$TextFilesInfo{ColToMergeLabels}[$Index]} = ();
+    push @{$TextFilesInfo{ColToMergeLabels}[$Index]}, @TextFilesColToMergeLabelsFiltered;
+  }
+}
+
+# Check SD file...
+sub ProcessSDFileInfo {
+  if (!CheckFileType($SDFile, "sd sdf")) {
+    die "Error: Invalid first file $SDFile: It's not a SD file\n";
+  }
+  if (!(-e $SDFile)) {
+    die "Error: SDFile $SDFile doesn't exist\n";
+  }
+}
+
+# Retrieve information about input text files...
+sub RetrieveTextFilesInfo {
+  my($Index, $TextFile, $FileDir, $FileName, $FileExt, $InDelim, $Line, $ColNum, $ColLabel, $FileNotOkayCount, @ColLabels,);
+
+  %TextFilesInfo = ();
+
+  @{$TextFilesInfo{FileOkay}} = ();
+  @{$TextFilesInfo{ColCount}} = ();
+  @{$TextFilesInfo{ColLabels}} = ();
+  @{$TextFilesInfo{ColLabelToNumMap}} = ();
+  @{$TextFilesInfo{InDelim}} = ();
+
+  $FileNotOkayCount = 0;
+
+  FILELIST: for $Index (0 .. $#TextFilesList) {
+    $TextFile = $TextFilesList[$Index];
+
+    $TextFilesInfo{FileOkay}[$Index] = 0;
+    $TextFilesInfo{ColCount}[$Index] = 0;
+    $TextFilesInfo{InDelim}[$Index] = "";
+
+    @{$TextFilesInfo{ColLabels}[$Index]} = ();
+    %{$TextFilesInfo{ColLabelToNumMap}[$Index]} = ();
+
+    if (!(-e $TextFile)) {
+      warn "Warning: Ignoring file $TextFile: It doesn't exist\n";
+      $FileNotOkayCount++;
+      next FILELIST;
+    }
+    if (!CheckFileType($TextFile, "csv tsv")) {
+      warn "Warning: Ignoring file $TextFile: It's not a csv or tsv file\n";
+      $FileNotOkayCount++;
+      next FILELIST;
+    }
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFile);
+    if ($FileExt =~ /^tsv$/i) {
+      $InDelim = "\t";
+    }
+    else {
+      $InDelim = "\,";
+      if ($OptionsInfo{InDelim} !~ /^(comma|semicolon)$/i) {
+	warn "Warning: Ignoring file $TextFile: The value specified, $OptionsInfo{InDelim}, for option \"--indelim\" is not valid for csv files\n";
+	$FileNotOkayCount++;
+	next FILELIST;
+      }
+      if ($OptionsInfo{InDelim} =~ /^semicolon$/i) {
+	$InDelim = "\;";
+      }
+    }
+
+    if (!open TEXTFILE, "$TextFile") {
+      warn "Warning: Ignoring file $TextFile: Couldn't open it: $! \n";
+      $FileNotOkayCount++;
+      next FILELIST;
+    }
+
+    $Line = GetTextLine(\*TEXTFILE);
+    @ColLabels = quotewords($InDelim, 0, $Line);
+    close TEXTFILE;
+
+    $TextFilesInfo{FileOkay}[$Index] = 1;
+    $TextFilesInfo{InDelim}[$Index] = $InDelim;
+
+    $TextFilesInfo{ColCount}[$Index] = @ColLabels;
+    push @{$TextFilesInfo{ColLabels}[$Index]}, @ColLabels;
+    for $ColNum (0 .. $#ColLabels) {
+      $ColLabel = $ColLabels[$ColNum];
+      $TextFilesInfo{ColLabelToNumMap}[$Index]{$ColLabel} = $ColNum;
+    }
+  }
+  # Make sure all specified files are valid for merging to work properly...
+  if ($FileNotOkayCount) {
+    die "Error: Problems with input text file(s)...\n";
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+  my($Index, $FileDir, $FileName, $FileExt, $NewSDFile, @ColValues, @KeyValues);
+
+  %OptionsInfo = ();
+
+  $OptionsInfo{Mode} = $Options{mode};
+
+  $OptionsInfo{Columns} = $Options{columns};
+  @{$OptionsInfo{ColValues}} = ();
+
+  if ($Options{columns}) {
+    @ColValues = split ";", $Options{columns};
+    if (@ColValues != @TextFilesList) {
+      die "Error: Invalid number of values specified by \"-c --columns\" option: it must be equal to number of input text files.\n";
+    }
+    for $Index (0 .. $#ColValues) {
+      if (!length($ColValues[$Index])) {
+	die "Error: Invalid value specified by \"-c --columns\" option: empty values are not allowed.\n";
+      }
+    }
+    @{$OptionsInfo{ColValues}} = @ColValues;
+  }
+
+  $OptionsInfo{Keys} = $Options{keys};
+  @{$OptionsInfo{KeyValues}} = ();
+
+  if ($Options{keys}) {
+    @KeyValues = split ";", $Options{keys};
+    if (@KeyValues != @TextFilesList) {
+      die "Error: Invalid number of values specified by \"-k --keys\" option: it must be equal to number of input text files.\n";
+    }
+    for $Index (0 .. $#KeyValues) {
+      if (!length($KeyValues[$Index])) {
+	die "Error: Invalid value specified by \"-k --keys\" option: empty values are not allowed.\n";
+      }
+    }
+    @{$OptionsInfo{KeyValues}} = @KeyValues;
+  }
+
+  $OptionsInfo{InDelim} = $Options{indelim};
+
+  $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
+  $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
+
+  $OptionsInfo{SDKey} = defined $Options{sdkey} ? $Options{sdkey} : undef;
+
+  # Setup new SD file...
+  if ($Options{root}) {
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root});
+    if ($FileName && $FileExt) {
+      $NewSDFile = $FileName;
+    }
+    else {
+      $NewSDFile =  $Options{root};
+    }
+  }
+  else {
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
+
+    $NewSDFile = $FileName;
+    ($FileDir, $FileName, $FileExt) = ParseFileName($TextFilesList[0]);
+
+    $NewSDFile = $NewSDFile . "MergedWith" . $FileName . "1To" . @TextFilesList;
+  }
+
+  $NewSDFile = $NewSDFile . ".sdf";
+  if (!$Options{overwrite}) {
+    if (-e $NewSDFile) {
+      die "Error: The file $NewSDFile already exists.\n";
+    }
+  }
+  if ($Options{root}) {
+    if (lc($NewSDFile) eq lc($SDFile)) {
+      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";
+    }
+  }
+  $OptionsInfo{NewSDFile} = $NewSDFile;
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{mode} = "colnum";
+  $Options{indelim} = "comma";
+
+  if (!GetOptions(\%Options, "help|h", "indelim=s", "columns|c=s", "keys|k=s", "mode|m=s", "overwrite|o", "root|r=s", "sdkey|s=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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{mode} !~ /^(colnum|collabel)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: colnum, or collabel\n";
+  }
+  if ($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{sdkey} && !$Options{keys}) {
+    die "Error: The option \"-s --sdkey\" can't be specified without the \"-k --keys\" option.\n";
+  }
+  elsif (!$Options{sdkey} && $Options{keys}) {
+    die "Error: The option \"-k --keys\" can't be specified without the \"-s --sdkey\" option.\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+MergeTextFilesWithSD.pl - Merge CSV or TSV TextFile(s) into SDFile
+
+=head1 SYNOPSIS
+
+MergeTextFilesWithSD.pl  SDFile TextFile(s)...
+
+MergeTextFilesWithSD.pl  [B<-h, --help>] [B<--indelim> comma | semicolon]
+[B<-c, --columns> colnum,...;... | collabel,...;...] [B<-k, --keys> colkeynum;... | colkeylabel;...]
+[B<-m, --mode> colnum | collabel] [B<-o, --overwrite>] [B<-r, --root> rootname]
+[B<-s, --sdkey> sdfieldname] [B<-w, --workingdir> dirname] SDFile TextFile(s)...
+
+=head1 DESCRIPTION
+
+Merge multiple CSV or TSV I<TextFile(s)> into I<SDFile>. Unless B<-k --keys>
+option is used, data rows from all I<TextFile(s)> are added to I<SDFile> in a
+sequential order, and the number of compounds in I<SDFile> is used to determine
+how many rows of data are added from I<TextFile(s)>.
+
+Multiple I<TextFile(s)> names are separated by spaces. 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<-h, --help>
+
+Print this help message.
+
+=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<-c, --columns> I<colnum,...;... | collabel,...;...>
+
+This value is mode specific. It is a list of columns to merge into I<SDFile>
+specified by column numbers or labels for each text file delimited by ";".
+All I<TextFile(s)> are merged into I<SDFile>.
+
+Default value: I<all;all;...>. By default, all columns from TextFile(s) are
+merged into I<SDFile>.
+
+For I<colnum> mode, input value format is: I<colnum,...;colnum,...;...>. Example:
+
+    "1,2;1,3,4;7,8,9"
+
+For I<collabel> mode, input value format is: I<collabel,...;collabel,...;...>. Example:
+
+    "MW,SumNO;SumNHOH,ClogP,PSA;MolName,Mol_Id,Extreg"
+
+=item B<-k, --keys> I<colkeynum;... | colkeylabel;...>
+
+This value is mode specific. It specifies column keys to use for merging
+I<TextFile(s)> into I<SDFile>. The column keys, delimited by ";", are specified by column
+numbers or labels for I<TextFile(s)>.
+
+By default, data rows from I<TextFile(s)> are merged into I<SDFile> in the order they appear.
+
+For I<colnum> mode, input value format is:I<colkeynum, colkeynum;...>. Example:
+
+    "1;3;7"
+
+For I<collabel> mode, input value format is:I<colkeylabel, colkeylabel;...>. Example:
+
+    "Mol_Id;Mol_Id;Cmpd_Id"
+
+=item B<-m, --mode> I<colnum | collabel>
+
+Specify how to merge I<TextFile(s)> into I<SDFile>: using column numbers or column labels.
+Possible values: I<colnum or collabel>. Default value: I<colnum>.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<-r, --root> I<rootname>
+
+New SD file name is generated using the root: <Root>.sdf. Default file name:
+<InitialSDFileName>MergedWith<FirstTextFileName>1To<Count>.sdf.
+
+=item B<-s, --sdkey> I<sdfieldname>
+
+I<SDFile> data field name used as a key to merge data from TextFile(s). By default,
+data rows from I<TextFile(s)> are merged into I<SDFile> in the order they appear.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To merge Sample1.csv and Sample2.csv into Sample.sdf and generate
+NewSample.sdf, type:
+
+    % MergeTextFileswithSD.pl -r NewSample -o Sample.sdf
+      Sample1.csv Sample2.csv
+
+To merge all Sample*.tsv into Sample.sdf and generate NewSample.sdf file, type:
+
+    % MergeTextFilesWithSD.pl -r NewSample -o Sample.sdf
+      Sample*.tsv
+
+To merge column numbers "1,2" and "3,4,5" from Sample2.csv and Sample3.csv
+into Sample.sdf and to generate NewSample.sdf, type:
+
+    % MergeTextFilesWithSD.pl -r NewSample -m colnum -c "1,2;3,4,5"
+      -o Sample.sdf Sample1.csv Sample2.csv
+
+To merge column "Mol_ID,Formula,MolWeight" and "Mol_ID,ChemBankID,NAME"
+from Sample1.csv and Sample2.csv into Sample.sdf using "Mol_ID" as SD and column keys
+to generate NewSample.sdf, type:
+
+    % MergeTextFilesWithSD.pl -r NewSample -s Mol_ID -k "Mol_ID;Mol_ID"
+      -m collabel -c "Mol_ID,Formula,MolWeight;Mol_ID,ChemBankID,NAME"
+      -o Sample1.sdf Sample1.csv Sample2.csv
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+ExtractFromSDFiles.pl, FilterSDFiles.pl, InfoSDFiles.pl, JoinSDFiles.pl, JoinTextFiles.pl,
+MergeTextFiles.pl, ModifyTextFilesFormat.pl, SplitSDFiles.pl, SplitTextFiles.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