#
# $Id: SwissPfam.pm 16123 2009-09-17 12:57:27Z cjfields $
#
# BioPerl module for Bio::Index::SwissPfam
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Index::SwissPfam - Interface for indexing swisspfam files
=head1 SYNOPSIS
use Bio::Index::SwissPfam;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name,
'-write_flag' => 'WRITE');
$inx->make_index(@ARGV);
use Bio::Index::SwissPfam;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns stream
while( <$seq> ) {
if(/^>/) {
print;
last;
}
}
}
=head1 DESCRIPTION
SwissPfam is one of the flat files released with Pfam. This modules
provides a way of indexing this module.
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and
provides the basic funtionallity for indexing SwissPfam files. Only
retrieves FileStreams at the moment. Once we have something better
(ie, an object!), will use that. Heavily snaffled from Index::Fasta system of
James Gilbert. Note: for best results 'use strict'.
=head1 FEED_BACK
=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://bioperl.org/wiki/Mailing_lists - About the mailing lists
=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:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Ewan Birney
Email - birney@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let's begin the code...
package Bio::Index::SwissPfam;
use strict;
use Bio::Seq;
use base qw(Bio::Index::Abstract);
sub _version {
return 0.1;
}
=head2 _index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index swisspfam format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
=cut
sub _index_file {
my( $self,
$file, # File name
$i # Index-number of file being indexed
) = @_;
my( $begin, # Offset from start of file of the start
# of the last found record.
$end, # Offset from start of file of the end
# of the last found record.
$id, # ID of last found record.
$acc, # accession of last record. Also put into the index
$nid, $nacc, # new ids for the record just found
);
$begin = 0;
$end = 0;
open my $SP, '<', $file or $self->throw("Can't open file for read : $file");
# Main indexing loop
while (<$SP>) {
if (/^>(\S+)\s+\|=*\|\s+(\S+)/) {
$nid = $1;
$nacc = $2;
my $new_begin = tell($SP) - length( $_ );
$end = $new_begin - 1;
if( $id ) {
$self->add_record($id, $i, $begin, $end);
if( $acc ne $id ) {
$self->add_record($acc, $i, $begin, $end);
}
}
$begin = $new_begin;
$id = $nid;
$acc = $nacc;
}
}
# Don't forget to add the last record
$end = tell($SP);
$self->add_record($id, $i, $begin, $end) if $id;
close $SP;
return 1;
}
=head2 fetch
Title : fetch
Usage : $index->fetch( $id )
Function: Returns a Bio::Seq object from the index
Example : $seq = $index->fetch( 'dJ67B12' )
Returns : Bio::Seq object
Args : ID
=cut
sub fetch {
my( $self, $id ) = @_;
my $desc;
my $db = $self->db();
if (my $rec = $db->{ $id }) {
my( @record );
my ($file, $begin, $end) = $self->unpack_record( $rec );
# Get the (possibly cached) filehandle
my $fh = $self->_file_handle( $file );
# move to start
seek($fh, $begin, 0);
return $fh;
} else {
$self->throw("Unable to find a record for $id in SwissPfam flat file index");
}
}
1;