Raw content of Bio::AlignIO::psi
<![CDATA[# $Id: psi.pm,v 1.6 2002/12/23 19:36:39 jason Exp $
#
# BioPerl module for Bio::AlignIO::psi
#
# 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::psi - Read/Write PSI-BLAST profile alignment files
=head1 SYNOPSIS
This module will parse PSI-BLAST output of the format seqid XXXX
=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::AlignIO::psi;
use vars qw(@ISA $BlockLen $IdLength);
use strict;
$BlockLen = 100;
$IdLength = 13;
# Object preamble - inherits from Bio::Root::Root
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::LocatableSeq;
@ISA = qw(Bio::AlignIO);
=head2 new
Title : new
Usage : my $obj = new Bio::AlignIO::psi();
Function: Builds a new Bio::AlignIO::psi object
Returns : Bio::AlignIO::psi
Args :
=cut
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : L<Bio::Align::AlignI> object
Args : NONE
=cut
sub next_aln {
my ($self) = @_;
my $aln;
my %seqs;
my @order;
while( defined ($_ = $self->_readline ) ) {
next if( /^\s+$/);
if( !defined $aln ) {
$aln = new Bio::SimpleAlign;
}
my ($id,$s) = split;
push @order, $id if( ! defined $seqs{$id});
$seqs{$id} .= $s;
}
foreach my $id ( @order) {
my $seq = new Bio::LocatableSeq(-seq => $seqs{$id},
-id => $id,
-start => 1,
-end => length($seqs{$id}));
$aln->add_seq($seq);
}
return $aln;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the NCBI psi-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,$aln) = @_;
unless( defined $aln && ref($aln) &&
$aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a valid Bio::Align::AlignI to write_aln");
return 0;
}
my $ct = 0;
my @seqs = $aln->each_seq;
my $len = 1;
my $alnlen = $aln->length;
my $idlen = $IdLength;
my @ids = map { substr($_->display_id,0,$idlen) } @seqs;
while( $len < $alnlen ) {
my $start = $len;
my $end = $len + $BlockLen;
if( $end > $alnlen ) { $end = $alnlen; }
my $c = 0;
foreach my $seq ( @seqs ) {
$self->_print(sprintf("%-".$idlen."s %s\n",
$ids[$c++],
$seq->subseq($start,$end)));
}
$self->_print("\n");
$len += $BlockLen+1;
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
]]>