#
# BioPerl module for FAST::Bio::AlignIO::prodom
# based on the FAST::Bio::SeqIO::prodom module
# by Ewan Birney <birney@ebi.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
FAST::Bio::AlignIO::prodom - prodom sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the L<FAST::Bio::AlignIO> class.
=head1 DESCRIPTION
This object can transform L<FAST::Bio::Align::AlignI> objects to and from prodom flat
file databases.
=head1 FEEDBACK
=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
the bugs and their resolution. Bug reports can be submitted via the
web:
=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...
use strict;
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Returns : L<FAST::Bio::Align::AlignI> object
Args : NONE
=cut
sub next_aln {
my $self = shift;
my $entry;
my ($acc, $fake_id, $start, $end, $seq, $add, %names);
my $aln = FAST::Bio::SimpleAlign->new(-source => 'prodom');
while( $entry = $self->_readline) {
if ($entry =~ /^AC\s+(\S+)\s*$/) { #ps 9/12/00
$aln->id( $1 );
}
elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){ #ps 9/12/00
$acc=$1;
$fake_id=$2; # Accessions have _species appended
$start=$3;
$end=$4;
$seq=$5;
$names{'fake_id'} = $fake_id;
$add = FAST::Bio::LocatableSeq->new('-seq' => $seq,
'-id' => $acc,
'-start' => $start,
'-end' => $end,
'-alphabet' => $self->alphabet,
);
$aln->add_seq($add);
}
elsif ($entry =~ /^CO/) {
# the consensus line marks the end of the alignment part of the entry
last;
}
}
return $aln if $aln->num_sequences;
return;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in prodom format ###Not yet implemented!###
Returns : 1 for success and 0 for error
Args : L<FAST::Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
$self->throw_not_implemented();
}
1;