Raw content of Bio::SeqIO::pir
<![CDATA[# $Id: pir.pm,v 1.18 2002/10/25 16:23:16 jason Exp $
#
# BioPerl module for Bio::SeqIO::PIR
#
# Cared for by Aaron Mackey <amackey@virginia.edu>
#
# Copyright Aaron Mackey
#
# You may distribute this module under the same terms as perl itself
#
# _history
# October 18, 1999 Largely rewritten by Lincoln Stein
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::pir - PIR sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from pir flat
file databases.
Note: This does not completely preserve the PIR format - quality
information about sequence is currently discarded since bioperl
does not have a mechanism for handling these encodings in sequence
data.
=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 one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.shtml - About the mailing lists
=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
Aaron Mackey E<lt>amackey@virginia.eduE<gt>
Lincoln Stein E<lt>lstein@cshl.orgE<gt>
Jason Stajich E<lt>jason@bioperl.orgE<gt>
=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::SeqIO::pir;
use vars qw(@ISA);
use strict;
use Bio::SeqIO;
use Bio::Seq::SeqFactory;
@ISA = qw(Bio::SeqIO);
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
if( ! defined $self->sequence_factory ) {
$self->sequence_factory(new Bio::Seq::SeqFactory
(-verbose => $self->verbose(),
-type => 'Bio::Seq'));
}
}
=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
=cut
sub next_seq {
my ($self) = @_;
local $/ = "\n>";
return unless my $line = $self->_readline;
if( $line eq '>' ) { # handle the very first one having no comment
return unless $line = $self->_readline;
}
my ($top, $desc,$seq) = ( $line =~ /^(.+?)\n(.+?)\n([^>]*)/s ) or
$self->throw("Cannot parse entry PIR entry [$line]");
my ( $type,$id ) = ( $top =~ /^>?([PF])1;(\S+)\s*$/ ) or
$self->throw("PIR stream read attempted without leading '>P1;' [ $line ]");
# P - indicates complete protein
# F - indicates protein fragment
# not sure how to stuff these into a Bio object
# suitable for writing out.
$seq =~ s/\*//g;
$seq =~ s/[\(\)\.\/\=\,]//g;
$seq =~ s/\s+//g; # get rid of whitespace
my ($alphabet) = ('protein');
# TODO - not processing SFS data
return $self->sequence_factory->create
(-seq => $seq,
-primary_id => $id,
-id => $type. '1;' . $id,
-desc => $desc,
-alphabet => $alphabet
);
}
=head2 write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objects
=cut
sub write_seq {
my ($self, @seq) = @_;
for my $seq (@seq) {
$self->throw("Did not provide a valid Bio::PrimarySeqI object")
unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
my $str = $seq->seq();
return unless $self->_print(">".$seq->id(),
"\n", $seq->desc(), "\n",
$str, "*\n");
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
]]>