view variant_effect_predictor/Bio/Index/SwissPfam.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

#
# $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 <[e-mail]>
#
# 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.

  [e-mail]             - 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:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Ewan Birney

Email - [e-mail]

=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 <[e-mail]> 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;