Raw content of Bio::Index::SwissPfam
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#
# $Id: SwissPfam.pm,v 1.15 2002/10/22 07:38:33 lapp Exp $
#
# BioPerl module for Bio::Index::SwissPfam
#
# 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( <$seq> ) {
if(/^>/) {
print;
last;
}
}
}
=head1 DESCRIPTION
SwissPfam is one of the flat files released with Pfam. This modules
provides a way of indexing this module.
Inherits functions for managing dbm files from
Bio::Index::Abstract.pm, and provides the basic funtionallity for
indexing SwissPfam files. Only retrieves FileStreams at the
moment. Once we have something better (ie, an object!), will use
that. Heavily snaffled from James Gilbert's Fasta system. Note: for
best results 'use strict'.
=head1 FEED_BACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney
Email - birney@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let's begin the code...
package Bio::Index::SwissPfam;
use vars qw($VERSION @ISA);
use strict;
use Bio::Index::Abstract;
use Bio::Seq;
@ISA = qw(Bio::Index::Abstract);
#
# Suggested fix by Michael G Schwern <schwern@pobox.com> to
# get around a clash with CPAN shell...
#
BEGIN {
$VERSION = 0.1;
}
sub _version {
return $VERSION;
}
=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 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;
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