Summary

Bio::Index::Swissprot - Interface for indexing (multiple) Swissprot
.dat files (ie flat file swissprot format).

Package variables

Included modules

Inherit

Bio::Index::AbstractSeq

Synopsis

    # Complete code for making an index for several
    # Swissprot files
    use Bio::Index::Swissprot;
    use strict;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::Swissprot->new('-filename' => $Index_File_Name, 
					 '-write_flag' => 'WRITE');
    $inx->make_index(@ARGV);

    # Print out several sequences present in the index
    # in gcg format
    use Bio::Index::Swissprot;
    use Bio::SeqIO;
    use strict;

    my $out = Bio::SeqIO->new( '-format' => 'gcg', '-fh' => \*STDOUT );
    my $Index_File_Name = shift;
    my $inx = Bio::Index::Swissprot->new('-filename' => $Index_File_Name);

    foreach my $id (@ARGV) {
        my $seq = $inx->fetch($id); # Returns Bio::Seq object
        $out->write_seq($seq);
    }

    # alternatively

    my $seq1 = $inx->get_Seq_by_id($id);
    my $seq2 = $inx->get_Seq_by_acc($acc);

Description

Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
and provides the basic funtionallity for indexing Swissprot files, and
retrieving the sequence from them. Heavily snaffled from James Gilbert's
Fasta system. Note: for best results 'use strict'.

Methods

Methods description

  Title   : _index_file
  Usage   : $index->_index_file( $file_name, $i )
  Function: Specialist function to index Swissprot format files.
            Is provided with a filename and an integer
            by make_index in its SUPER class.
  Example : 
  Returns : 
  Args    :

 Title   : _file_format
 Usage   : Internal function for indexing system
 Function: Provides file format for this database
 Example :
 Returns : 
 Args    :

Methods code

BEGIN {

    $VERSION = 0.1;

}

sub _type_stamp {

    return '__Swissprot_FLAT__'; # What kind of index are we?

}

sub _version {

    return $VERSION;

}

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.
        $id,    # ID of last found record.
	@accs,   # accession of last record. Also put into the index
        );

    $begin = 0;

    open SWISSPROT, $file or $self->throw("Can't open file for read : $file");

    # Main indexing loop
    $id = undef;
    @accs = ();
    while (<SWISSPROT>) {
	if( /^\/\// ) {
	    if( ! defined $id ) {
		$self->throw("Got to a end of entry line for an Swissprot flat file with no parsed ID. Considering this a problem!");
		next;
	    }
	    if( ! @accs ) {
		$self->warn("For id [$id] in Swissprot flat file, got no accession number. Storing id index anyway");
	    }

	    $self->add_record($id, $i, $begin);

	    foreach my $acc (@accs) {
		if( $acc ne $id ) {
		    $self->add_record($acc, $i, $begin);
		}
	    }
	    @accs = ();    # reset acc array
	    $id = undef;   # reset id
	} elsif (/^ID\s+(\S+)/) {
	    $id = $1;
	    # not sure if I like this. Assummes tell is in bytes.
	    # we could tell before each line and save it.
            $begin = tell(SWISSPROT) - length( $_ ); 
	    
	} elsif (/^AC(.*)/) { # ignore ? if there.
	    push(@accs, ($1 =~ /\s*(\S+);/g));
	} else {
	    # do nothing
	}
    }

    close SWISSPROT;
    return 1;

}

sub _file_format {

   my ($self,@args) = @_;

   return 'swiss';

}

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://bio.perl.org/MailList.html    - 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
(Swissprot adaption: lorenz@ist.org)

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