Raw content of Bio::Search::HSP::FastaHSP
<![CDATA[# $Id: FastaHSP.pm,v 1.4.2.1 2003/02/28 09:47:19 jason Exp $
#
# BioPerl module for Bio::Search::HSP::FastaHSP
#
# 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::Search::HSP::FastaHSP - HSP object for FASTA specific data
=head1 SYNOPSIS
# get a FastaHSP from a SearchIO stream
my $in = new Bio::SearchIO(-format => 'fasta', -file => 'filename.fasta');
while( my $r = $in->next_result) {
while( my $hit = $r->next_result ) {
while( my $hsp = $hit->next_hsp ) {
print "smith-waterman score (if available): ",
$hsp->sw_score(),"\n";
}
}
}
=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::Search::HSP::FastaHSP;
use vars qw(@ISA);
use strict;
use Bio::Search::HSP::GenericHSP;
@ISA = qw(Bio::Search::HSP::GenericHSP );
=head2 new
Title : new
Usage : my $obj = new Bio::Search::HSP::FastaHSP();
Function: Builds a new Bio::Search::HSP::FastaHSP object
Returns : Bio::Search::HSP::FastaHSP
Args : -swscore => smith-waterman score
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($swscore) = $self->_rearrange([qw(SWSCORE)], @args);
defined $swscore && $self->sw_score($swscore);
return $self;
}
=head2 sw_score
Title : sw_score
Usage : $obj->sw_score($newval)
Function: Get/Set Smith-Waterman score
Returns : value of sw_score
Args : newvalue (optional)
=cut
sub sw_score{
my ($self,$value) = @_;
if( defined $value || ! defined $self->{'_sw_score'} ) {
$value = 0 unless defined $value; # default value
$self->{'_sw_score'} = $value;
}
return $self->{'_sw_score'};
}
sub get_aln {
my ($self) = @_;
require Bio::LocatableSeq;
require Bio::SimpleAlign;
my $aln = new Bio::SimpleAlign;
my $hs = $self->hit_string();
my $qs = $self->query_string();
# fasta reports some extra 'regional' sequence information
# we need to clear out first
# this seemed a bit insane to me at first, but it appears to
# work --jason
# we infer the end of the regional sequence where the first
# non space is in the homology string
# then we use the HSP->length to tell us how far to read
# to cut off the end of the sequence
my ($start) = 0;
if( $self->homology_string() =~ /^(\s+)/ ) {
$start = CORE::length($1);
}
$self->debug("hs seq is '$hs'\n");
$self->debug("qs seq is '$qs'\n");
$hs = substr($hs, $start,$self->length('total'));
$qs = substr($qs, $start,$self->length('total'));
foreach my $seq ( $qs,$hs) {
foreach my $f ( '\\', '/', ' ') {
my $index = index($seq,$f);
while( $index >=0 && length($seq) > 0 ) {
substr($hs,$index,1) = '';
substr($qs,$index,1) = '';
$self->debug( "$f, $index+1, for ".length($seq). " ($seq)\n");
$index = index($seq,$f,$index+1);
}
}
}
my $seqonly = $qs;
$seqonly =~ s/[\-\s]//g;
my ($q_nm,$s_nm) = ($self->query->seq_id(),
$self->hit->seq_id());
unless( defined $q_nm && CORE::length ($q_nm) ) {
$q_nm = 'query';
}
unless( defined $s_nm && CORE::length ($s_nm) ) {
$s_nm = 'hit';
}
my $query = new Bio::LocatableSeq('-seq' => $qs,
'-id' => $q_nm,
'-start' => 1,
'-end' => CORE::length($seqonly),
);
$seqonly = $hs;
$seqonly =~ s/[\-\s]//g;
my $hit = new Bio::LocatableSeq('-seq' => $hs,
'-id' => $s_nm,
'-start' => 1,
'-end' => CORE::length($seqonly),
);
$aln->add_seq($query);
$aln->add_seq($hit);
return $aln;
}
1;
]]>