#
# BioPerl module for Bio::Align::PairwiseStatistics
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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
use strict;
my $stats = Bio::Align::PairwiseStatistics->new();
# get alignment object of two sequences somehow
my $pwaln;
print $stats->number_of_comparable_bases($pwaln);
my $score = $stats->score_nuc($pwaln);
=head1 DESCRIPTION
Calculate pairwise statistics.
=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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=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($GapChars);
use strict;
BEGIN { $GapChars = '(\.|\-)'; }
use base 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 : L<Bio::Align::AlignI>
=cut
sub number_of_comparable_bases{
my ($self,$aln) = @_;
if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->throw("Must provide a Bio::Align::AlignI compliant object to ".
"Bio::Align::PairwiseStatistics");
return 0;
} elsif ( $aln->num_sequences != 2 ) {
$self->throw("Only pairwise calculations supported. Found ".
$aln->num_sequences." sequences in alignment\n");
}
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 sequences
Returns : integer
Args : L<Bio::Align::AlignI>
=cut
sub number_of_differences{
my ($self,$aln) = @_;
if( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->throw("Must provide a Bio::Align::AlignI compliant object to ".
"Bio::Align::PairwiseStatistics");
} elsif ( $aln->num_sequences != 2 ) {
$self->throw("Only pairwise calculations supported. Found ".
$aln->num_sequences." sequences in alignment\n");
}
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 gapped positions among sequences in alignment
Returns : integer
Args : L<Bio::Align::AlignI>
=cut
sub number_of_gaps{
my ($self,$aln) = @_;
if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->throw("Must provide a Bio::Align::AlignI compliant object to ".
"Bio::Align::PairwiseStatistics");
} elsif ( $aln->num_sequences != 2 ) {
$self->throw("Only pairwise calculations supported. Found ".
$aln->num_sequences." sequences in alignment\n");
}
my $gapline = $aln->gap_line;
# this will count the number of '-' characters
return $gapline =~ tr/-/-/;
}
=head2 score_nuc
Title : score_nuc
Usage : my $score = $stat->score_nuc($aln);
or
my $score = $stat->score_nuc(
-aln =>$aln,
-match => 1,
-mismatch => -1,
-gap_open => -1,
-gap_ext => -1
);
Function: Calculate the score of an alignment of 2 nucleic acid sequences. The
scoring parameters can be specified. Otherwise the blastn default
parameters are used: match = 2, mismatch = -3, gap opening = -5, gap
extension = -2
Returns : alignment score (number)
Args : L<Bio::Align::AlignI>
match score [optional]
mismatch score [optional]
gap opening score [optional]
gap extension score [optional]
=cut
sub score_nuc {
my ($self, @args) = @_;
my ( $aln, $match, $mismatch, $gap_open, $gap_ext) = $self->_rearrange( [qw(
ALN MATCH MISMATCH GAP_OPEN GAP_EXT)], @args );
if ( ! defined $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->throw("Must provide a Bio::Align::AlignI compliant object to ".
"Bio::Align::PairwiseStatistics");
} elsif ( $aln->num_sequences != 2 ) {
$self->throw("Only pairwise calculations supported. Found ".
$aln->num_sequences." sequences in alignment\n");
}
my $seq1 = $aln->get_seq_by_pos(1);
my $seq2 = $aln->get_seq_by_pos(2);
if (! ( ($seq1->alphabet eq 'dna' || $seq1->alphabet eq 'rna') &&
($seq2->alphabet eq 'dna' || $seq2->alphabet eq 'rna') )) {
$self->throw("Can only score nucleic acid alignments");
}
$match ||= 2; # Blastn scoring defaults
$mismatch ||= -3;
$gap_open ||= -5;
$gap_ext ||= -2;
my $score = 0;
my $prevres1 = '-';
my $prevres2 = '-';
for (my $pos = 1 ; $pos <= $aln->length ; $pos++) {
my $res1 = $seq1->subseq($pos, $pos);
my $res2 = $seq2->subseq($pos, $pos);
if (!($res1 eq '-' || $res2 eq '-')) { # no gap
if ($res1 eq $res2) { # same residue
$score += $match;
} else { # other residue
$score += $mismatch;
}
} else { # open or ext gap?
my $open = 0;
if (!($res1 eq '-' && $res2 eq '-')) { # exactly one gap
my $prevres = $prevres1;
$prevres = $prevres2 if $res2 eq '-';
$open = 1 unless $prevres eq '-';
} else { # 2 gaps
$open = 1 unless $prevres1 eq '-' && $prevres2 eq '-';
}
if ($open) {
$score += $gap_open; # gap opening
} else {
$score += $gap_ext; # gap extension
}
}
$prevres1 = $res1;
$prevres2 = $res2;
}
return $score;
}
1;