Summary

Bio::Index::SwissPfam - Interface for indexing swisspfam files

Package variables

Included modules

Inherit

Bio::Index::Abstract

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;
	    }
	}
    }

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'.
Details on configuration and additional example code are available in the
biodatabases.pod file.

Methods

Methods description

  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    :

  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

Methods code

sub _version {

    return 0.1;

}

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;

}

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");
    }

}

General documentation

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

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/

Email - birney@sanger.ac.uk

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _