Raw content of Bio::Align::PairwiseStatistics
<![CDATA[# $Id: PairwiseStatistics.pm,v 1.2 2002/10/22 07:45:10 lapp Exp $
#
# BioPerl module for Bio::Align::PairwiseStatistics
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
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/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Align::PairwiseStatistics;
use vars qw(@ISA $GapChars);
use strict;
use Bio::Align::StatisticsI;
use Bio::Root::Root;
BEGIN { $GapChars = '(\.|\-)'; }
@ISA = qw(Bio::Root::Root Bio::Align::StatisticsI );
=head2 number_of_comparable_bases
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
=cut
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");
}
my $L = $aln->length - $self->number_of_gaps($aln);
return $L;
}
=head2 number_of_differences
Title : number_of_differences
Usage : my $nd = $stat->number_of_distances($aln);
Function: Returns the number of differences between two
Returns : integer
Args : Bio::Align::AlignI
=cut
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;
}
=head2 number_of_gaps
Title : number_of_gaps
Usage : my $nd = $stat->number_of_gaps($aln);
Function: Returns the number of differences between two
Example :
Returns :
Args :
=cut
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;
} 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 $gapcount = 0;
for (my $i = 0;$i<$aln->length; $i++ ) {
($gapcount++) && next if( $firstseq->[$i] =~ /^$GapChars$/);
foreach my $seq ( @seqs ) {
($gapcount++) && next if( $seq->[$i] =~ /^$GapChars$/);
}
}
return $gapcount;
}
1;
]]>