Raw content of Bio::AlignIO::fasta
<![CDATA[# $Id: fasta.pm,v 1.11 2002/12/14 19:09:05 birney Exp $
#
# BioPerl module for Bio::AlignIO::fasta
# based on the Bio::SeqIO::fasta module
# 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::fasta - FastA MSA 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 L<Bio::SimpleAlign> objects to and from
fasta flat file databases. This is for the fasta sequence format NOT
FastA analysis program. To process the pairwise alignments from a
FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.
=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::fasta;
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 - returns 0 on end of file
or on error
Args : NONE
=cut
sub next_aln {
my $self = shift;
my $entry;
my ($start,$end,$name,$seqname,$seq,$seqchar,$tempname,%align);
my $aln = Bio::SimpleAlign->new();
while(defined ($entry = $self->_readline)) {
if($entry =~ /^>(\S+)/ ) {
$tempname = $1;
if( defined $name ) {
# put away last name and sequence
if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
$seqname = $1;
$start = $2;
$end = $3;
} else {
$seqname=$name;
$start = 1;
$end = length($seqchar); #ps 9/6/00
}
# print STDERR "Going to add with $seqchar $seqname\n";
$seq = new Bio::LocatableSeq('-seq'=>$seqchar,
'-id'=>$seqname,
'-start'=>$start,
'-end'=>$end,
);
$aln->add_seq($seq);
}
$name = $tempname;
$seqchar = "";
next;
}
$entry =~ s/[^A-Za-z\.\-]//g;
$seqchar .= $entry;
}
#
# Next two lines are to silence warnings that
# otherwise occur at EOF when using <$fh>
if (!defined $name) {$name="";}
if (!defined $seqchar) {$seqchar="";}
# Put away last name and sequence
if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
$seqname = $1;
$start = $2;
$end = $3;
} else {
$seqname=$name;
$start = 1;
$end = length($seqchar); #ps 9/6/00
# $end = length($align{$name});
}
# 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 $aln;}
# This logic now also reads empty lines at the
# end of the file. Skip this is seqchar and seqname is null
if( length($seqchar) == 0 && length($seqname) == 0 ) {
# skip
} else {
# print STDERR "end to add with $seqchar $seqname\n";
$seq = new Bio::LocatableSeq('-seq'=>$seqchar,
'-id'=>$seqname,
'-start'=>$start,
'-end'=>$end,
);
$aln->add_seq($seq);
}
return $aln;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
my ($seq,$rseq,$name,$count,$length,$seqsub);
foreach my $aln (@aln) {
if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
next;
}
foreach $rseq ( $aln->each_seq() ) {
$name = $aln->displayname($rseq->get_nse());
$seq = $rseq->seq();
$self->_print (">$name\n") or return ;
$count =0;
$length = length($seq);
while( ($count * 60 ) < $length ) {
$seqsub = substr($seq,$count*60,60);
$self->_print ("$seqsub\n") or return ;
$count++;
}
}
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
]]>