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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/ExtractFromSequenceFiles.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,590 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: ExtractFromSequenceFiles.pl,v $
+# $Date: 2015/02/28 20:46:19 $
+# $Revision: 1.23 $
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use SequenceFileUtil;
+
+my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
+
+# Autoflush STDOUT
+$| = 1;
+
+# Starting message...
+$ScriptName = basename($0);
+print "\n$ScriptName: Starting...\n\n";
+$StartTime = new Benchmark;
+
+# Setup script usage message...
+SetupScriptUsage();
+if ($Options{help} || @ARGV < 1) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+# Expand wild card file names...
+my(@SequenceFilesList);
+@SequenceFilesList = ExpandFileNames(\@ARGV, "aln msf fasta fta pir");
+
+# Process options...
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+# Set up information about input files...
+print "Checking input sequence file(s)...\n";
+my(%SequenceFilesInfo);
+RetrieveSequenceFilesInfo();
+
+# Process input files..
+my($FileIndex);
+if (@SequenceFilesList > 1) {
+  print "\nProcessing sequence files...\n";
+}
+for $FileIndex (0 .. $#SequenceFilesList) {
+  if ($SequenceFilesInfo{FilesOkay}[$FileIndex]) {
+    print "\nProcessing file $SequenceFilesList[$FileIndex]...\n";
+    ExtractFromSequenceFiles($FileIndex);
+  }
+}
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Extract from sequence files...
+sub ExtractFromSequenceFiles {
+  my($FileIndex) = @_;
+  my($OutSequenceFile, $SequenceFile, $SequenceDataRef, $SpecifiedSequenceDataRef);
+
+  # Read sequence file...
+  $SequenceFile = $SequenceFilesList[$FileIndex];
+  open SEQUENCEFILE, "$SequenceFile" or die "Error: Can't open $SequenceFile: $! \n";
+  $SequenceDataRef = ReadSequenceFile($SequenceFile);
+  close SEQUENCEFILE;
+
+  $OutSequenceFile = $SequenceFilesInfo{OutFile}[$FileIndex];
+  print "Generating sequence file $OutSequenceFile...\n";
+
+  # Retrieve sequence data for specified sequences...
+  $SpecifiedSequenceDataRef = GetSpecifiedSequenceData($SequenceDataRef);
+
+  # Handle gaps...
+  if ($OptionsInfo{IgnoreGaps}) {
+    if (@{$SpecifiedSequenceDataRef->{IDs}} > 1) {
+      if (AreSequenceLengthsIdentical($SpecifiedSequenceDataRef)) {
+	$SpecifiedSequenceDataRef = RemoveSequenceAlignmentGapColumns($SpecifiedSequenceDataRef);
+      }
+    }
+    else {
+      # Remove the gaps from the sequence...
+      my($ID, $Sequence);
+      $ID = $SpecifiedSequenceDataRef->{IDs}[0];
+      $Sequence = $SpecifiedSequenceDataRef->{Sequence}{$ID};
+      $SpecifiedSequenceDataRef->{Sequence}{$ID} = RemoveSequenceGaps($Sequence);
+    }
+  }
+
+  # Write out the file...
+  WritePearsonFastaSequenceFile($OutSequenceFile, $SpecifiedSequenceDataRef, $OptionsInfo{MaxSequenceLength});
+}
+
+# Get specified sequence data...
+sub GetSpecifiedSequenceData {
+  my($SequenceDataRef) = @_;
+
+  if ($OptionsInfo{Mode} =~ /^SequenceID$/i) {
+    return GetDataBySequenceIDs($SequenceDataRef);
+  }
+  elsif ($Options{mode} =~ /^SequenceNum$/i) {
+    return GetDataBySequenceNums($SequenceDataRef);
+  }
+  elsif ($Options{mode} =~ /^SequenceNumRange$/i) {
+    return GetDataBySequenceNumRange($SequenceDataRef);
+  }
+  else {
+    return undef;
+  }
+}
+
+# Get specified sequence data...
+sub GetDataBySequenceIDs {
+  my($SequenceDataRef) = @_;
+  my($ID, $SequenceCount, $IDMatched, $SpecifiedID, %SpecifiedSequenceDataMap);
+
+  # Go over sequences and collect sequences for writing out a new sequence file...
+  %SpecifiedSequenceDataMap = ();
+  @{$SpecifiedSequenceDataMap{IDs}} = ();
+  %{$SpecifiedSequenceDataMap{Description}} = ();
+  %{$SpecifiedSequenceDataMap{Sequence}} = ();
+
+  $SequenceCount = 0;
+  ID: for $ID (@{$SequenceDataRef->{IDs}}) {
+    if ($OptionsInfo{MatchExactSequenceIDs}) {
+      if (!exists $OptionsInfo{SpecifiedSequenceIDsMap}{lc($ID)}) {
+	next ID;
+      }
+      if ($SequenceCount >= scalar @{$OptionsInfo{SpecifiedSequenceIDs}}) {
+	last ID;
+      }
+      $SequenceCount++;
+    }
+    else {
+      # Does this ID contains specified ID as substring...
+      $IDMatched = 0;
+      SPECIFIEDID: for $SpecifiedID (@{$OptionsInfo{SpecifiedSequenceIDs}}) {
+	if ($ID =~ /$SpecifiedID/i) {
+	  $IDMatched = 1;
+	  last SPECIFIEDID;
+	}
+      }
+      if (!$IDMatched) {
+	next ID;
+      }
+      $SequenceCount++;
+    }
+    # Collect sequence data...
+    push @{$SpecifiedSequenceDataMap{IDs}}, $ID;
+    $SpecifiedSequenceDataMap{Description}{$ID} = $SequenceDataRef->{Description}{$ID};
+    $SpecifiedSequenceDataMap{Sequence}{$ID} = $SequenceDataRef->{Sequence}{$ID};
+  }
+
+  return \%SpecifiedSequenceDataMap;
+}
+
+# Get specified sequence data...
+sub GetDataBySequenceNums {
+  my($SequenceDataRef) = @_;
+  my($ID, $SequenceNum, $SequenceCount, %SpecifiedSequenceDataMap);
+
+  # Go over sequences and collect sequences for writing out a new sequence file...
+  %SpecifiedSequenceDataMap = ();
+  @{$SpecifiedSequenceDataMap{IDs}} = ();
+  %{$SpecifiedSequenceDataMap{Description}} = ();
+  %{$SpecifiedSequenceDataMap{Sequence}} = ();
+
+  $SequenceNum = 0;
+  $SequenceCount = 0;
+  ID: for $ID (@{$SequenceDataRef->{IDs}}) {
+    $SequenceNum++;
+    if (!exists $OptionsInfo{SpecifiedSequenceIDsMap}{$SequenceNum}) {
+      next ID;
+    }
+    if ($SequenceCount >= scalar @{$OptionsInfo{SpecifiedSequenceIDs}}) {
+      last ID;
+    }
+    $SequenceCount++;
+
+    # Collect sequence data...
+    push @{$SpecifiedSequenceDataMap{IDs}}, $ID;
+    $SpecifiedSequenceDataMap{Description}{$ID} = $SequenceDataRef->{Description}{$ID};
+    $SpecifiedSequenceDataMap{Sequence}{$ID} = $SequenceDataRef->{Sequence}{$ID};
+  }
+
+  return \%SpecifiedSequenceDataMap;
+}
+
+# Get specified sequence data...
+sub GetDataBySequenceNumRange {
+  my($SequenceDataRef) = @_;
+  my($ID, $SequenceNum, $SequenceCount, %SpecifiedSequenceDataMap);
+
+  # Go over sequences and collect sequences for writing out a new sequence file...
+  %SpecifiedSequenceDataMap = ();
+  @{$SpecifiedSequenceDataMap{IDs}} = ();
+  %{$SpecifiedSequenceDataMap{Description}} = ();
+  %{$SpecifiedSequenceDataMap{Sequence}} = ();
+
+  $SequenceNum = 0;
+  $SequenceCount = 0;
+  ID: for $ID (@{$SequenceDataRef->{IDs}}) {
+    $SequenceNum++;
+
+    if (!($SequenceNum >= $OptionsInfo{SpecifiedSequenceIDs}[0] && $SequenceNum <= $OptionsInfo{SpecifiedSequenceIDs}[1])) {
+      next ID;
+    }
+    if ($SequenceNum > $OptionsInfo{SpecifiedSequenceIDs}[1]) {
+      last ID;
+    }
+    $SequenceCount++;
+    # Collect sequence data...
+    push @{$SpecifiedSequenceDataMap{IDs}}, $ID;
+    $SpecifiedSequenceDataMap{Description}{$ID} = $SequenceDataRef->{Description}{$ID};
+    $SpecifiedSequenceDataMap{Sequence}{$ID} = $SequenceDataRef->{Sequence}{$ID};
+  }
+
+  return \%SpecifiedSequenceDataMap;
+}
+
+
+# Process option values...
+sub ProcessOptions {
+  %OptionsInfo = ();
+
+  # Miscellaneous options...
+  $OptionsInfo{IgnoreGaps} = ($Options{ignoregaps} =~ /Yes/i) ? 1 : 0;
+
+  $OptionsInfo{Mode} = $Options{mode};
+  $OptionsInfo{MatchExactSequenceIDs} = $Options{sequenceidmatch} =~ /Exact/i ? 1 :0;
+
+  # Check specified sequences value...
+  $OptionsInfo{SpecifiedSequences} = $Options{sequences};
+  @{$OptionsInfo{SpecifiedSequenceIDs}} = ();
+  %{$OptionsInfo{SpecifiedSequenceIDsMap}} = ();
+
+  my(@SpecifiedSequenceIDs) = ();
+  if ($Options{mode} =~ /^SequenceID$/i) {
+    if (!$Options{sequences}) {
+      die "Error: No value specified for option \"-s, --Sequences\" during \"SequenceID\" of \"-m, --mode\" option\n";
+    }
+    @SpecifiedSequenceIDs = split /\,/, $Options{sequences};
+  }
+  elsif ($Options{mode} =~ /^SequenceNum$/i) {
+    if ($Options{sequences}) {
+      @SpecifiedSequenceIDs = split /\,/, $Options{sequences};
+      my($SequenceNum);
+      for $SequenceNum (@SpecifiedSequenceIDs) {
+	if (!IsPositiveInteger($SequenceNum)) {
+	  die "Error: The value specified, $SequenceNum, in \"$Options{sequences}\" for option \"-s, --Sequences\" is not valid: Valid values: > 0\n";
+	}
+      }
+    }
+    else {
+      push @SpecifiedSequenceIDs, "1";
+    }
+  }
+  elsif ($Options{mode} =~ /^SequenceNumRange$/i) {
+    if (!$Options{sequences}) {
+      die "Error: No value specified for option \"-s, --Sequences\" during \"SequenceNumRange\" of \"-m, --mode\" option\n";
+    }
+    @SpecifiedSequenceIDs = split /\,/, $Options{sequences};
+    if (@SpecifiedSequenceIDs != 2) {
+      die "Error: The number of values", scalar @SpecifiedSequenceIDs, " specified, $Options{sequences}, for option \"-s, --Sequences\" are not valid. Number of values must be 2 to indicate starting and ending sequence number.\n";
+    }
+    my($SequenceNum);
+    for $SequenceNum (@SpecifiedSequenceIDs) {
+      if (!IsPositiveInteger($SequenceNum)) {
+	die "Error: The value specified, $SequenceNum, in \"$Options{sequences}\" for option \"-s, --Sequences\" is not valid: Valid values: > 0\n";
+      }
+    }
+    if ($SpecifiedSequenceIDs[0] > $SpecifiedSequenceIDs[1]) {
+      die "Error: The value specified \"$Options{sequences}\" for option \"-s, --Sequences\" are not valid: Starting sequence number $SpecifiedSequenceIDs[0] must be smaller than ending sequence number $SpecifiedSequenceIDs[1]\n";
+    }
+  }
+  push @{$OptionsInfo{SpecifiedSequenceIDs}}, @SpecifiedSequenceIDs;
+  my($SequenceID);
+  for $SequenceID (@SpecifiedSequenceIDs) {
+    if ($Options{mode} =~ /^SequenceID$/i) {
+      $OptionsInfo{SpecifiedSequenceIDsMap}{lc($SequenceID)} = $SequenceID;
+    }
+    else {
+      $OptionsInfo{SpecifiedSequenceIDsMap}{$SequenceID} = $SequenceID;
+    }
+  }
+
+  $OptionsInfo{MaxSequenceLength} = $Options{sequencelength};
+  $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
+  $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
+}
+
+# Retrieve information about sequence files...
+sub RetrieveSequenceFilesInfo {
+  my($Index, $SequenceFile, $FileSupported, $FileFormat, $SequenceCount, $FileDir, $FileName, $FileExt, $OutFileRoot, $OutFileExt, $OutFileMode, $SequenceDataRef);
+
+  %SequenceFilesInfo = ();
+  @{$SequenceFilesInfo{FilesOkay}} = ();
+  @{$SequenceFilesInfo{OutFileRoot}} = ();
+  @{$SequenceFilesInfo{OutFileExt}} = ();
+  @{$SequenceFilesInfo{OutFile}} = ();
+  @{$SequenceFilesInfo{Format}} = ();
+  @{$SequenceFilesInfo{SequenceCount}} = ();
+
+  FILELIST: for $Index (0 .. $#SequenceFilesList) {
+    $SequenceFile = $SequenceFilesList[$Index];
+    $SequenceFilesInfo{FilesOkay}[$Index] = 0;
+    $SequenceFilesInfo{OutFileRoot}[$Index] = '';
+    $SequenceFilesInfo{OutFileExt}[$Index] = '';
+    $SequenceFilesInfo{OutFile}[$Index] = '';
+    $SequenceFilesInfo{Format}[$Index] = 'NotSupported';
+    $SequenceFilesInfo{SequenceCount}[$Index] = 0;
+
+    if (! open SEQUENCEFILE, "$SequenceFile") {
+      warn "Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+    close SEQUENCEFILE;
+
+    ($FileSupported, $FileFormat) = IsSupportedSequenceFile($SequenceFile);
+    if (!$FileSupported) {
+      warn "Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n";
+      next FILELIST;
+    }
+    $SequenceDataRef = ReadSequenceFile($SequenceFile);
+
+    $SequenceCount = $SequenceDataRef->{Count};
+    if (!$SequenceCount) {
+      warn "Warning: Ignoring file $SequenceFile: Sequence data is missing.\n";
+      next FILELIST;
+    }
+
+    # Setup output file names...
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SequenceFile);
+    $OutFileExt = 'fasta';
+    if ($OptionsInfo{OutFileRoot} && (@SequenceFilesList == 1)) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
+      if ($RootFileName && $RootFileExt) {
+	$FileName = $RootFileName;
+      }
+      else {
+	$FileName = $OptionsInfo{OutFileRoot};
+      }
+      $OutFileRoot = $FileName;
+    }
+    else {
+      $OutFileRoot = $FileName;
+    }
+    MODE: {
+	if ($OptionsInfo{Mode} =~ /^SequenceID$/i) { $OutFileMode = 'SequenceID'; last MODE;}
+	if ($OptionsInfo{Mode} =~ /^SequenceNum$/i) { $OutFileMode = 'SequenceNum'; last MODE;}
+	if ($OptionsInfo{Mode} =~ /^SequenceNumRange$/i) { $OutFileMode = 'SequenceNumRange'; last MODE;}
+	$OutFileMode = '';
+    }
+    if (!$OptionsInfo{OverwriteFiles}) {
+      if (-e "${OutFileRoot}${OutFileMode}.${OutFileExt}") {
+	warn "Warning: Ignoring file $SequenceFile: The file ${OutFileRoot}${OutFileMode}.${OutFileExt} already exists\n";
+	next FILELIST;
+      }
+    }
+
+    $SequenceFilesInfo{FilesOkay}[$Index] = 1;
+    $SequenceFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
+    $SequenceFilesInfo{OutFileExt}[$Index] = $OutFileExt;
+    $SequenceFilesInfo{OutFile}[$Index] = "${OutFileRoot}${OutFileMode}.${OutFileExt}";
+
+    $SequenceFilesInfo{Format}[$Index] = $FileFormat;
+    $SequenceFilesInfo{SequenceCount}[$Index] = $SequenceCount;
+  }
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{ignoregaps} = 'Yes';
+  $Options{mode} = 'SequenceNum';
+  $Options{sequenceidmatch} = 'Relaxed';
+  $Options{sequencelength} = 80;
+
+  if (!GetOptions(\%Options, "help|h", "ignoregaps|i=s", "mode|m=s", "overwrite|o", "root|r=s", "sequences|s=s", "sequenceidmatch=s", "sequencelength=i", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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{ignoregaps} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{ignoregaps}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
+  }
+  if ($Options{mode} !~ /^(SequenceID|SequenceNum|SequenceNumRange)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: SequenceID, SequenceNum, or SequenceNumRange\n";
+  }
+  if ($Options{sequenceidmatch} !~ /^(Exact|Relaxed)$/i) {
+    die "Error: The value specified, $Options{sequenceidmatch}, for option \"--SequenceIDMatch\" is not valid. Allowed values: Exact or Relaxed\n";
+  }
+  if (!IsPositiveInteger($Options{sequencelength})) {
+    die "Error: The value specified, $Options{sequencelength}, for option \"--SequenceLength\" is not valid. Allowed values: >0\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+ExtractFromSequenceFiles.pl - Extract data from sequence and alignment files
+
+=head1 SYNOPSIS
+
+ExtractFromSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...
+
+ExtractFromSequenceFiles.pl [B<-h, --help>] [B<-i, --IgnoreGaps> yes | no]
+[B<-m, --mode> SequenceID | SequenceNum | SequenceNumRange] [B<-o, --overwrite>]
+[B<-r, --root> rootname] [B<-s, --Sequences> "SequenceID, [SequenceID,...]" | "SequenceNum, [SequenceNum,...]" |
+"StartingSeqNum, EndingSeqNum"] [B<--SequenceIDMatch> Exact | Relaxed]
+[B<-w, --WorkingDir> dirname] SequenceFile(s) AlignmentFile(s)...
+
+=head1 DESCRIPTION
+
+Extract specific data from I<SequenceFile(s) and AlignmentFile(s)> and generate
+FASTA files. You can extract sequences using sequence IDs or sequence numbers.
+
+The file names are separated by spaces. All the sequence files in a current directory can
+be specified by I<*.aln>, I<*.msf>, I<*.fasta>, I<*.fta>, I<*.pir> or any other supported
+formats; additionally, I<DirName> corresponds to all the sequence files in the current directory
+with any of the supported file extension: I<.aln, .msf, .fasta, .fta, and .pir>.
+
+Supported sequence formats are: I<ALN/CLustalW>, I<GCG/MSF>, I<PILEUP/MSF>, I<Pearson/FASTA>,
+and I<NBRF/PIR>. Instead of using file extensions, file formats are detected by parsing the contents
+of I<SequenceFile(s) and AlignmentFile(s)>.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<-i, --IgnoreGaps> I<yes | no>
+
+Ignore gaps or gap columns during during generation of new sequence or alignment file(s).
+Possible values: I<yes or no>. Default value: I<yes>.
+
+In order to remove gap columns, length of all the sequence must be same; otherwise,
+this option is ignored.
+
+=item B<-m, --mode> I<SequenceID | SequenceNum | SequenceNumRange>
+
+Specify how to extract data from sequence files: extract sequences using sequence
+IDs or sequence numbers. Possible values: I<SequenceID | SequenceNum
+| SequenceNumRange>. Default: I<SequenceNum> with value of 1.
+
+The sequence numbers correspond to position of sequences starting from 1 for first sequence
+in I<SequenceFile(s) and AlignmentFile(s)>.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<-r, --root> I<rootname>
+
+New sequence file name is generated using the root: <Root><Mode>.<Ext>. Default new file:
+<SequenceFileName><Mode>.<Ext>. This option is ignored for multiple input files.
+
+=item B<-s, --Sequences> I<"SequenceID,[SequenceID,...]" | "SequenceNum,[SequenceNum,...]" | "StartingSeqNum,EndingSeqNum">
+
+This value is B<-m, --mode> specific. In general, it's a comma delimites list of sequence IDs or sequence
+numbers.
+
+For I<SequenceID> value of B<-m, --mode> option, input value format is: I<SequenceID,...>. Examples:
+
+    ACHE_BOVIN
+    ACHE_BOVIN,ACHE_HUMAN
+
+For I<SequenceNum> value of B<-m, --mode> option, input value format is: I<SequenceNum,...>. Examples:
+
+    2
+    1,5
+
+For I<SequenceNum> value of B<-m, --mode> option, input value format is: I<StaringSeqNum,EndingSeqNum>. Examples:
+
+    2,4
+
+=item B<--SequenceIDMatch> I<Exact | Relaxed>
+
+Sequence IDs matching criterion during I<SequenceID> value of B<-m, --mode> option: match
+specified sequence ID exactly or as sub string against sequence IDs in the files. Possible
+values: I<Exact | Relaxed>. Default: I<Relaxed>. Sequence ID match is case insenstitive
+during both options.
+
+=item B<--SequenceLength> I<number>
+
+Maximum sequence length per line in sequence file(s). Default: I<80>.
+
+=item B<-w --WorkingDir> I<text>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To extract first sequence from Sample1.fasta sequence file and generate Sample1SequenceNum.fasta
+sequence file, type:
+
+    % ExtractFromSequenceFiles.pl -o Sample1.fasta
+
+To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta
+sequence file without any column gaps, type:
+
+    % ExtractFromSequenceFiles.pl -o Sample1.aln
+
+To extract first sequence from Sample1.aln alignment file and generate Sample1SequenceNum.fasta
+sequence file with column gaps, type:
+
+    % ExtractFromSequenceFiles.pl --IgnroreGaps No -o Sample1.aln
+
+To extract sequence number 1 and 4 from Sample1.fasta sequence file and generate
+Sample1SequenceNum.fasta sequence file, type:
+
+    % ExtractFromSequenceFiles.pl -o -m SequenceNum --Sequences 1,4
+      -o Sample1.fasta
+
+To extract sequences from sequence  number 1 to 4 from Sample1.fasta sequence file and generate
+Sample1SequenceNumRange.fasta sequence file, type:
+
+    % ExtractFromSequenceFiles.pl -o -m SequenceNumRange --Sequences
+      1,4 -o Sample1.fasta
+
+To extract sequence ID "Q9P993/104-387" from sequence  from Sample1.fasta sequence file and generate
+Sample1SequenceID.fasta sequence file, type:
+
+    % ExtractFromSequenceFiles.pl -o -m SequenceID --Sequences
+      "Q9P993/104-387" --SequenceIDMatch Exact -o Sample1.fasta
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+AnalyzeSequenceFilesData.pl, InfoSequenceFiles.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