[Bioperl-l] Converting Genbank to fasta via SeqIO

[Wes Barris]

Hi,

I am using the following code to convert a genbank file into a fasta
file:

my $seq_in = Bio::SeqIO->new('-file' => "<$infile", '-format' => 'genbank');
my $seq_out = Bio::SeqIO->new('-file' => ">$outfile", '-format' => 'fasta');

while ( my $inseq = $seq_in->next_seq ) {
    if ($seq->accession =~ '_') {
       $seq_out->write_seq($inseq);
    }
}

The genbank entry (NM_174198) results in the following defline
in the fasta file:

 >TLR4 Bos taurus toll-like receptor 4 (TLR4), mRNA.

However, I prefer to have a defline containing the accession number similar to
what is shown at the NCBI site:

 >gi|31342611|ref|NM_174198.2| Bos taurus toll-like receptor 4 (TLR4), mRNA

Is there a way to have the SeqIO routines do this?

-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au