Raw content of Bio::AlignIO::emboss
<![CDATA[# $Id: emboss.pm,v 1.11 2002/10/22 07:45:10 lapp Exp $
#
# BioPerl module for Bio::AlignIO::emboss
#
# 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::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
=head1 SYNOPSIS
# do not use the object directly
use Bio::AlignIO;
# read in an alignment from the EMBOSS program water
my $in = new Bio::AlignIO(-format => 'emboss',
-file => 'seq.water');
while( my $aln = $in->next_aln ) {
# do something with the alignment
}
=head1 DESCRIPTION
This object handles parsing and writing pairwise sequence alignments
from the EMBOSS suite.
=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::AlignIO::emboss;
use vars qw(@ISA $EMBOSSTitleLen $EMBOSSLineLen);
use strict;
use Bio::AlignIO;
use Bio::LocatableSeq;
@ISA = qw(Bio::AlignIO );
BEGIN {
$EMBOSSTitleLen = 13;
$EMBOSSLineLen = 50;
}
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
$self->{'_type'} = undef;
}
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
or on error
Args : NONE
=cut
sub next_aln {
my ($self) = @_;
my $seenbegin = 0;
my %data = ( 'seq1' => {
'start'=> undef,
'end'=> undef,
'name' => '',
'data' => '' },
'seq2' => {
'start'=> undef,
'end'=> undef,
'name' => '',
'data' => '' },
'align' => '',
'type' => $self->{'_type'}, # to restore type from
# previous aln if possible
);
my %names;
while( defined($_ = $self->_readline) ) {
next if( /^\#?\s+$/ || /^\#+\s*$/ );
if( /^\#(\=|\-)+\s*$/) {
last if( $seenbegin);
} elsif( /(Local|Global):\s*(\S+)\s+vs\s+(\S+)/ ||
/^\#\s+Program:\s+(\S+)/ )
{
my ($name1,$name2) = ($2,$3);
if( ! defined $name1 ) { # Handle EMBOSS 2.2.X
$data{'type'} = $1;
$name1 = $name2 = '';
} else {
$data{'type'} = $1 eq 'Local' ? 'water' : 'needle';
}
$data{'seq1'}->{'name'} = $name1;
$data{'seq2'}->{'name'} = $name2;
$self->{'_type'} = $data{'type'};
} elsif( /Score:\s+(\S+)/ ) {
$data{'score'} = $1;
} elsif( /^\#\s+(1|2):\s+(\S+)/ && ! $data{"seq$1"}->{'name'} ) {
my $nm = $2;
$nm = substr($nm,0,$EMBOSSTitleLen); # emboss has a max seq length
if( $names{$nm} ) {
$nm .= "-". $names{$nm};
}
$names{$nm}++;
$data{"seq$1"}->{'name'} = $nm;
} elsif( $data{'seq1'}->{'name'} &&
/^$data{'seq1'}->{'name'}/ ) {
my $count = 0;
$seenbegin = 1;
my @current;
while( defined ($_) ) {
my $align_other = '';
my $delayed;
if($count == 0 || $count == 2 ) {
my @l = split;
my ($seq,$align,$start,$end);
if( $count == 2 && $data{'seq2'}->{'name'} eq '' ) {
# weird boundary condition
($start,$align,$end) = @l;
} elsif( @l == 3 ) {
$align = '';
($seq,$start,$end) = @l
} else {
($seq,$start,$align,$end) = @l;
}
my $seqname = sprintf("seq%d", ($count == 0) ? '1' : '2');
$data{$seqname}->{'data'} .= $align;
$data{$seqname}->{'start'} ||= $start;
$data{$seqname}->{'end'} = $end;
$current[$count] = [ $start,$align || ''];
} else {
s/^\s+//;
s/\s+$//;
$data{'align'} .= $_;
}
BOTTOM:
last if( $count++ == 2);
$_ = $self->_readline();
}
if( $data{'type'} eq 'needle' ) {
# which ever one is shorter we want to bring it up to
# length. Man this stinks.
my ($s1,$s2) = ($data{'seq1'}, $data{'seq2'});
my $d = length($current[0]->[1]) - length($current[2]->[1]);
if( $d < 0 ) { # s1 is smaller, need to add some
# compare the starting points for this alignment line
if( $current[0]->[0] <= 1 && $current[2]->[0] > 1) {
$s1->{'data'} = ('-' x abs($d)) . $s1->{'data'};
$data{'align'} = (' 'x abs($d)).$data{'align'};
} else {
$s1->{'data'} .= '-' x abs($d);
$data{'align'} .= ' 'x abs($d);
}
} elsif( $d > 0) { # s2 is smaller, need to add some
if( $current[2]->[0] <= 1 && $current[0]->[0] > 1) {
$s2->{'data'} = ('-' x abs($d)) . $s2->{'data'};
$data{'align'} = (' 'x abs($d)).$data{'align'};
} else {
$s2->{'data'} .= '-' x abs($d);
$data{'align'} .= ' 'x abs($d);
}
}
}
}
}
return undef unless $seenbegin;
my $aln = Bio::SimpleAlign->new(-verbose => $self->verbose(),
-source => "EMBOSS-".$data{'type'});
foreach my $seqname ( qw(seq1 seq2) ) {
return undef unless ( defined $data{$seqname} );
$data{$seqname}->{'name'} ||= $seqname;
my $seq = new Bio::LocatableSeq('-seq' => $data{$seqname}->{'data'},
'-id' => $data{$seqname}->{'name'},
'-start'=> $data{$seqname}->{'start'},
'-end' => $data{$seqname}->{'end'},
);
$aln->add_seq($seq);
}
return $aln;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in emboss format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
$self->throw("Sorry: writing emboss output is not currently available! \n");
}
1;
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