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Bio::Index::Swissprot

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Bio::Index::Swissprot 1.4 is libraries software developed by Ewan Birney.
Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format).



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

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'.

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

Requirements:
Perl
Bio::Index::Swissprot 1.4 supports different languages (including english). It works with Linux.

Downloading Bio::Index::Swissprot 1.4 will take minute if you use fast ADSL connection.

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