Raw content of Bio::AlignIO::pfam
<![CDATA[# $Id: pfam.pm,v 1.10 2002/10/22 07:38:26 lapp Exp $
#
# BioPerl module for Bio::AlignIO::pfam
# based on the Bio::SeqIO:: modules
# by Ewan Birney <birney@sanger.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# and the SimpleAlign.pm module of Ewan Birney
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# _history
# September 5, 2000
# POD documentation - main docs before the code
=head1 NAME
Bio::AlignIO::pfam - pfam sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the L<Bio::AlignIO> class.
=head1 DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from pfam flat
file databases.
=head1 FEEDBACK
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHORS - Peter Schattner
Email: schattner@alum.mit.edu
=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::pfam;
use vars qw(@ISA);
use strict;
use Bio::AlignIO;
use Bio::SimpleAlign;
@ISA = qw(Bio::AlignIO);
=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 = shift;
my $entry;
my $name;
my $start;
my $end;
my $seq;
my $add;
my $acc;
my %names;
my $aln = Bio::SimpleAlign->new(-source => 'pfam');
while( $entry = $self->_readline) {
chomp $entry;
$entry =~ /^\/\// && last;
if($entry !~ /^(\S+)\/(\d+)-(\d+)\s+(\S+)\s*/ ) {
$self->throw("Found a bad line [$_] in the pfam format alignment");
next;
}
$name = $1;
$start = $2;
$end = $3;
$seq = $4;
$add = new Bio::LocatableSeq('-seq'=>$seq,
'-id'=>$name,
'-start'=>$start,
'-end'=>$end,
);
$aln->add_seq($add);
}
# If $end <= 0, we have either reached the end of
# file in <> or we have encountered some other error
#
if ($end <= 0) { undef $aln;}
return $aln;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
if( @aln > 1 ) { $self->warn("Only the 1st pfam alignment will be output since the format does not support multiple alignments in the same file"); }
my $aln = shift @aln;
if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
next;
}
my ($namestr,$seq,$add);
my ($maxn);
$maxn = $aln->maxdisplayname_length();
foreach $seq ( $aln->each_seq() ) {
$namestr = $aln->displayname($seq->get_nse());
$add = $maxn - length($namestr) + 2;
$namestr .= " " x $add;
$self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return;
}
$self->flush() if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
]]>