Summary

Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments

Package variables

Inherit

Bio::Align::StatisticsI Bio::Root::Root

Synopsis

  use strict;
  my $stats = Bio::Align::DNAStatistics->new();

  # get alignment object of two sequences somehow
  my $pwaln;
  print $stats->number_of_comparable_bases($pwaln);

Description

Calculate pairwise statistics.

Methods

Methods description

 Title   : number_of_comparable_bases
 Usage   : my $bases = $stat->number_of_comparable_bases($aln);
 Function: Returns the count of the number of bases that can be
           compared (L) in this alignment ( length - gaps)
 Returns : integer
 Args    : Bio::Align::AlignI

 Title   : number_of_differences
 Usage   : my $nd = $stat->number_of_distances($aln);
 Function: Returns the number of differences between two sequences
 Returns : integer
 Args    : Bio::Align::AlignI

 Title   : number_of_gaps
 Usage   : my $nd = $stat->number_of_gaps($aln);
 Function: Returns the number of gapped positions among sequences in alignment
 Returns : integer
 Args    : Bio::Align::AlignI

Methods code

BEGIN {

 $GapChars = '(\.|\-)';

}

sub number_of_comparable_bases {

   my ($self,$aln) = @_;
   if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
       $self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::PairwiseStatistics");
       return 0;
   } elsif( $aln->no_sequences != 2 ) { 
       $self->warn("only pairwise calculations currently supported ". $aln->no_sequences."\n");
   }
   my $L = $aln->length - $self->number_of_gaps($aln);
   return $L;

}

sub number_of_differences {

   my ($self,$aln) = @_;
    if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
	$self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::PairwiseStatistics");
	return 0;
    } elsif( $aln->no_sequences != 2 ) { 
	$self->warn("only pairwise calculations currently supported");
    }
   my (@seqs);
   foreach my $seq ( $aln->each_seq) {
       push @seqs, [ split(//,$seq->seq())];
   }
   my $firstseq = shift @seqs;
#    my $secondseq = shift @seqs;
   my $diffcount = 0;
   for (my $i = 0;$i<$aln->length; $i++ ) {
       next if( $firstseq->[$i]  =~ /^$GapChars$/);
       foreach my $seq ( @seqs ) {
	   next if( $seq->[$i]  =~ /^$GapChars$/);
	   if( $firstseq->[$i] ne $seq->[$i] ) {
	       $diffcount++;
	   }
       }
   }
   return $diffcount;

}

sub number_of_gaps {

   my ($self,$aln) = @_;
    if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
	$self->warn("Must provide a Bio::Align::AlignI compliant object to Bio::Align::PairwiseStatistics");
	return 0;
    }
   my $gapline = $aln->gap_line;
   # this will count the number of '-' characters
   return $gapline =~ tr/-/-/;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Email jason-at-bioperl-dot-org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _