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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/InfoSequenceFiles.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,471 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: InfoSequenceFiles.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $Revision: 1.29 $
+#
+# 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 "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use SequenceFileUtil;
+use StatisticsUtil;
+
+my($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(@SequenceFilesList);
+@SequenceFilesList = ExpandFileNames(\@ARGV, "aln msf fasta fta pir");
+
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+print "Checking input sequence file(s)...\n";
+my(%SequenceFilesInfo);
+RetrieveSequenceFilesInfo();
+
+my($FileIndex);
+if (@SequenceFilesList > 1) {
+  print "\nProcessing sequence files...\n";
+}
+for $FileIndex (0 .. $#SequenceFilesList) {
+  if ($SequenceFilesInfo{FileOkay}[$FileIndex]) {
+    print "\nProcessing file $SequenceFilesList[$FileIndex]...\n";
+    ListSequenceFileInfo($FileIndex);
+  }
+}
+ListTotalSizeOfFiles();
+
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# List appropriate information...
+sub ListSequenceFileInfo {
+  my($Index) = @_;
+  my($SequenceFile, $SequenceDataRef);
+
+  $SequenceFile = $SequenceFilesList[$Index];
+
+  $SequenceDataRef = ReadSequenceFile($SequenceFile);
+
+  my($SequencesCount) = $SequenceDataRef->{Count};
+  print "\nNumber of sequences: $SequencesCount\n";
+
+  if ($OptionsInfo{ListShortestSequence} && ($SequencesCount > 1)) {
+    my($ShortestSeqID, $ShortestSeq, $ShortestSeqLen, $Description) = GetShortestSequence($SequenceDataRef, $OptionsInfo{IgnoreGaps});
+    print "\nShortest sequence information:\nID: $ShortestSeqID; Length:$ShortestSeqLen\n";
+    if ($OptionsInfo{DetailLevel} >= 2) {
+      print "Description: $Description\n";
+    }
+    if ($OptionsInfo{DetailLevel} >= 3) {
+      print "Sequence: $ShortestSeq\n";
+    }
+  }
+  if ($OptionsInfo{ListLongestSequence} && ($SequencesCount > 1)) {
+    my($LongestSeqID, $LongestSeq, $LongestSeqLen, $Description) = GetLongestSequence($SequenceDataRef, $OptionsInfo{IgnoreGaps});
+    print "\nLongest sequence information:\nID: $LongestSeqID; Length: $LongestSeqLen\n";
+    if ($OptionsInfo{DetailLevel} >= 2) {
+      print "Description: $Description\n";
+    }
+    if ($OptionsInfo{DetailLevel} >= 3) {
+      print "Sequence: $LongestSeq\n";
+    }
+  }
+  if ($OptionsInfo{FrequencyAnalysis} && ($SequencesCount > 1)) {
+    PerformLengthFrequencyAnalysis($SequenceDataRef);
+  }
+  if ($OptionsInfo{ListSequenceLengths}) {
+    ListSequenceLengths($SequenceDataRef);
+  }
+
+  # File size and modification information...
+  print "\nFile size: ", FormatFileSize($SequenceFilesInfo{FileSize}[$Index]), " \n";
+  print "Last modified: ", $SequenceFilesInfo{FileLastModified}[$Index], " \n";
+}
+
+# List information about sequence lengths...
+sub ListSequenceLengths {
+  my($SequenceDataRef) = @_;
+  my($ID, $SeqLen, $Sequence, $Description);
+
+  print "\nSequence lengths information:\n";
+  for $ID (@{$SequenceDataRef->{IDs}}) {
+    $Sequence = $SequenceDataRef->{Sequence}{$ID};
+    $Description = $SequenceDataRef->{Description}{$ID};
+    $SeqLen = GetSequenceLength($Sequence, $OptionsInfo{IgnoreGaps});
+    if ($OptionsInfo{IgnoreGaps}) {
+      $Sequence = RemoveSequenceGaps($Sequence);
+    }
+    print "ID: $ID; Length:$SeqLen\n";
+    if ($OptionsInfo{DetailLevel} >= 2) {
+      print "Description: $Description\n";
+    }
+    if ($OptionsInfo{DetailLevel} >= 3) {
+      print "Sequence: $Sequence\n";
+    }
+    if ($OptionsInfo{DetailLevel} >= 2) {
+      print "\n";
+    }
+  }
+}
+
+# Total size of all the fiels...
+sub ListTotalSizeOfFiles {
+  my($FileOkayCount, $TotalSize, $Index);
+
+  $FileOkayCount = 0;
+  $TotalSize = 0;
+
+  for $Index (0 .. $#SequenceFilesList) {
+    if ($SequenceFilesInfo{FileOkay}[$Index]) {
+      $FileOkayCount++;
+      $TotalSize += $SequenceFilesInfo{FileSize}[$Index];
+    }
+  }
+  if ($FileOkayCount > 1) {
+    print "\nTotal size of $FileOkayCount files: ", FormatFileSize($TotalSize), "\n";
+  }
+}
+
+
+# Perform frequency analysis of sequence lengths
+sub PerformLengthFrequencyAnalysis {
+  my($SequenceDataRef, $SequenceLengthsRef) = @_;
+  my ($ID, $SeqLen, $Sequence, $SequenceLenBin, $LenBin, $SequenceLenCount, @SequenceLengths, %SequenceLenFrequency);
+
+  @SequenceLengths = ();
+  %SequenceLenFrequency = ();
+  for $ID (@{$SequenceDataRef->{IDs}}) {
+    $Sequence = $SequenceDataRef->{Sequence}{$ID};
+    $SeqLen = GetSequenceLength($Sequence, $OptionsInfo{IgnoreGaps});
+    push @SequenceLengths, $SeqLen;
+  }
+  if (@{$OptionsInfo{BinRange}}) {
+    %SequenceLenFrequency = Frequency(\@SequenceLengths, \@{$OptionsInfo{BinRange}});
+  }
+  else {
+    %SequenceLenFrequency = Frequency(\@SequenceLengths, $OptionsInfo{NumOfBins});
+  }
+  print "\nDistribution of sequence lengths (LengthBin => Count):\n";
+  for $SequenceLenBin (sort { $a <=> $b} keys %SequenceLenFrequency) {
+    $SequenceLenCount = $SequenceLenFrequency{$SequenceLenBin};
+    $LenBin = sprintf("%.1f", $SequenceLenBin) + 0;
+    print "$LenBin => $SequenceLenCount; ";
+  }
+  print "\n";
+}
+
+# Retrieve information about sequence files...
+sub RetrieveSequenceFilesInfo {
+  my($Index, $SequenceFile, $FileSupported, $FileFormat, $ModifiedTimeString, $ModifiedDateString);
+
+  %SequenceFilesInfo = ();
+  @{$SequenceFilesInfo{FileOkay}} = ();
+  @{$SequenceFilesInfo{FileFormat}} = ();
+  @{$SequenceFilesInfo{FileSize}} = ();
+  @{$SequenceFilesInfo{FileLastModified}} = ();
+
+  FILELIST: for $Index (0 .. $#SequenceFilesList) {
+    $SequenceFile = $SequenceFilesList[$Index];
+
+    if (! open SEQUENCEFILE, "$SequenceFile") {
+      warn "Warning: Ignoring file $SequenceFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+    close SEQUENCEFILE;
+
+    $SequenceFilesInfo{FileOkay}[$Index] = 0;
+    $SequenceFilesInfo{FileFormat}[$Index] = 'NotSupported';
+    $SequenceFilesInfo{FileSize}[$Index] = 0;
+    $SequenceFilesInfo{FileLastModified}[$Index] = '';
+
+    ($FileSupported, $FileFormat) = IsSupportedSequenceFile($SequenceFile);
+    if (!$FileSupported) {
+      warn "Warning: Ignoring file $SequenceFile: Sequence file format is not supported.\n";
+      next FILELIST;
+    }
+
+    $SequenceFilesInfo{FileOkay}[$Index] = 1;
+    $SequenceFilesInfo{FileFormat}[$Index] = $FileFormat;
+    $SequenceFilesInfo{FileSize}[$Index] = FileSize($SequenceFile);
+
+    ($ModifiedTimeString, $ModifiedDateString) = FormattedFileModificationTimeAndDate($SequenceFile);
+    $SequenceFilesInfo{FileLastModified}[$Index] = "$ModifiedTimeString; $ModifiedDateString";
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+
+  $OptionsInfo{All} = defined $Options{all} ? $Options{all} : undef;
+
+  $OptionsInfo{Count} = defined $Options{count} ? $Options{count} : undef;
+  $OptionsInfo{DetailLevel} = $Options{detail};
+  $OptionsInfo{Frequency} = defined $Options{frequency} ? $Options{frequency} : undef;
+  $OptionsInfo{FrequencyBins} = defined $Options{frequencybins} ? $Options{frequencybins} : undef;
+  $OptionsInfo{IgnoreGaps} = defined $Options{ignoregaps} ? $Options{ignoregaps} : undef;
+  $OptionsInfo{Longest} = defined $Options{longest} ? $Options{longest} : undef;
+  $OptionsInfo{Shortest} = defined $Options{shortest} ? $Options{shortest} : undef;
+  $OptionsInfo{SequenceLengths} = defined $Options{sequencelengths} ? $Options{sequencelengths} : undef;
+
+  $OptionsInfo{FrequencyAnalysis} = ($Options{all} || $Options{frequency}) ? 1 : 0;
+  $OptionsInfo{ListLongestSequence} = ($Options{all} || $Options{longest}) ? 1 : 0;
+  $OptionsInfo{ListShortestSequence} = ($Options{all} || $Options{shortest}) ? 1 : 0;
+  $OptionsInfo{ListSequenceLengths} = ($Options{all} || $Options{sequencelengths}) ? 1 : 0;
+  $OptionsInfo{IgnoreGaps} = ($Options{ignoregaps} =~ /Yes/i) ? 1 : 0;
+
+  # Setup frequency bin values...
+  $OptionsInfo{NumOfBins} = 4;
+  @{$OptionsInfo{BinRange}} = ();
+
+  if ($Options{frequencybins} =~ /\,/) {
+    my($BinValue, @SpecifiedBinRange);
+    @SpecifiedBinRange = split /\,/,  $Options{frequencybins};
+    if (@SpecifiedBinRange < 2) {
+      die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain at least two values. \n";
+    }
+    for $BinValue (@SpecifiedBinRange) {
+      if (!IsNumerical($BinValue)) {
+	die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Contains non numeric values. \n";
+      }
+    }
+    my($Index1, $Index2);
+    for $Index1 (0 .. $#SpecifiedBinRange) {
+      for $Index2 (($Index1 + 1) .. $#SpecifiedBinRange) {
+	if ($SpecifiedBinRange[$Index1] >= $SpecifiedBinRange[$Index2]) {
+	  die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid: Must contain values in ascending order. \n";
+	}
+      }
+    }
+    push @{$OptionsInfo{BinRange}}, @SpecifiedBinRange;
+  }
+  else {
+    $OptionsInfo{NumOfBins} = $Options{frequencybins};
+    if (!IsPositiveInteger($OptionsInfo{NumOfBins})) {
+      die "Error: The value specified, $Options{frequencybins}, for option \"--frequencybins\" is not valid. Allowed values: positive integer or \"number,number,[number]...\". \n";
+    }
+  }
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{detail} = 1;
+  $Options{ignoregaps} = 'no';
+  $Options{frequencybins} = 10;
+
+  if (!GetOptions(\%Options, "all|a", "count|c", "detail|d=i", "frequency|f", "frequencybins=s", "help|h", "ignoregaps|i=s", "longest|l", "shortest|s", "sequencelengths", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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}: $! \n";
+  }
+  if (!IsPositiveInteger($Options{detail})) {
+    die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
+  }
+  if ($Options{ignoregaps} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{ignoregaps}, for option \"-i --IgnoreGaps\" is not valid. Allowed values: yes or no\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+InfoSequenceFiles.pl - List information about sequence and alignment files
+
+=head1 SYNOPSIS
+
+InfoSequenceFiles.pl SequenceFile(s) AlignmentFile(s)...
+
+InfoSequenceFiles.pl [B<-a, --all>] [B<-c, --count>] [B<-d, --detail> infolevel]
+[B<-f, --frequency>] [B<--FrequencyBins> number | "number, number, [number,...]"]
+[B<-h, --help>] [B<-i, --IgnoreGaps> yes | no] [B<-l, --longest>] [B<-s, --shortest>]
+[B<--SequenceLengths>] [B<-w, --workingdir> dirname] SequenceFile(s)...
+
+=head1 DESCRIPTION
+
+List information about contents of I<SequenceFile(s) and AlignmentFile(s)>: number of sequences,
+shortest and longest sequences, distribution of sequence lengths and so on. 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<-a, --all>
+
+List all the available information.
+
+=item B<-c, --count>
+
+List number of of sequences. This is B<default behavior>.
+
+=item B<-d, --detail> I<InfoLevel>
+
+Level of information to print about sequences during various options. Default: I<1>.
+Possible values: I<1, 2 or 3>.
+
+=item B<-f, --frequency>
+
+List distribution of sequence lengths using the specified number of bins or bin range specified
+using B<FrequencyBins> option.
+
+This option is ignored for input files containing only single sequence.
+
+=item B<--FrequencyBins> I<number | "number,number,[number,...]">
+
+This value is used with B<-f, --frequency> option to list distribution of sequence lengths using
+the specified number of bins or bin range. Default value: I<10>.
+
+The bin range list is used to group sequence lengths  into different groups; It must contain
+values in ascending order. Examples:
+
+    100,200,300,400,500,600
+    200,400,600,800,1000
+
+The frequency value calculated for a specific bin corresponds to all the sequence lengths
+which are greater than the previous bin value and less than or equal to the current bin value.
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<-i, --IgnoreGaps> I<yes | no>
+
+Ignore gaps during calculation of sequence lengths. Possible values: I<yes or
+no>. Default value: I<no>.
+
+=item B<-l, --longest>
+
+List information about longest sequence: ID, sequence and sequence length. This option
+is ignored for input files containing only single sequence.
+
+=item B<-s, --shortest>
+
+List information about shortest sequence: ID, sequence and sequence length. This option
+is ignored for input files containing only single sequence.
+
+=item B<--SequenceLengths>
+
+List information about sequence lengths.
+
+=item B<-w, --WorkingDir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To count number of sequences in sequence files, type:
+
+    % InfoSequenceFiles.pl Sample1.fasta
+    % InfoSequenceFiles.pl Sample1.msf Sample1.aln Sample1.pir
+    % InfoSequenceFiles.pl *.fasta *.fta *.msf *.pir *.aln
+
+To list all available information with maximum level of available detail for a sequence
+alignment file Sample1.msf, type:
+
+    % InfoSequenceFiles.pl -a -d 3 Sample1.msf
+
+To list sequence length information after ignoring sequence gaps in Sample1.aln file, type:
+
+    % InfoSequenceFiles.pl --SequenceLengths --IgnoreGaps Yes
+      Sample1.aln
+
+To list shortest and longest sequence length information after ignoring sequence
+gaps in Sample1.aln file, type:
+
+    % InfoSequenceFiles.pl --longest --shortest --IgnoreGaps Yes
+      Sample1.aln
+
+To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and
+report the frequency distribution into 10 bins, type:
+
+    % InfoSequenceFiles.pl --frequency --FrequencyBins 10
+      --IgnoreGaps Yes Sample1.aln
+
+To list distribution of sequence lengths after ignoring sequence gaps in Sample1.aln file and
+report the frequency distribution into specified bin range, type:
+
+    % InfoSequenceFiles.pl --frequency --FrequencyBins
+      "150,200,250,300,350" --IgnoreGaps Yes Sample1.aln
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+AnalyzeSequenceFilesData.pl, ExtractFromSequenceFiles.pl, InfoAminoAcids.pl, InfoNucleicAcids.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