Bio::Index::Swissprot 1.4 review

Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS

License: Perl Artistic License File size: 4788K Developer: Ewan Birney

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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