Get the full FASTA header or Full GenPept record for retrieval

GenPept retrieval

#!/usr/bin/perl -w
# Jason Stajich jason<at>bioperl.org
use strict;
use Bio::DB::GenPept;
use Bio::DB::GenBank;
use Bio::SeqIO;

#  get the FASTA formatted header for BLAST database
my $db = Bio::DB::GenBank->new(-format => 'fasta');
my $out = Bio::SeqIO->new(-format => 'fasta');

my $seq = $db->get_Seq_by_id('NP_006959.1');
$out->write_seq($seq);


# get the full GenPept record
$db = Bio::DB::GenBank->new(-format => 'gp');
$out = Bio::SeqIO->new(-format => 'genbank');

$seq = $db->get_Seq_by_id('NP_006959.1');
$out->write_seq($seq);

# works when you use the wrong DB (genbank)
eval {
    $db = Bio::DB::GenBank->new(-format => 'gb');
    $out = Bio::SeqIO->new(-format => 'genbank');
    
    $seq = $db->get_Seq_by_id('NP_006959.1');
    $out->write_seq($seq);
};
if($@) {
    # should never get here
    warn("couldn't request a protein record from GenBank\n");
}