[Bioperl-l] Re: need help with large genbank file (Chris Dagdigian)

[darin.m.london@gsk.com]

Dinakar
I thought of one more thing.  If the file is zipped up using gzip, or if
you can gzip it and gunzip it.  You might zip it, and then feed a pipe from
gunzip -c to it.


#!/usr/bin/env perl

use lib '/home/desas2/perl_mod/lib/site_perl/5.6.0/';

use Bio::SeqIO;

$seqio = Bio::SeqIO->new( -file =>'gunzip -c /home/desas2/data/nt.gz', '
-format' =>
'Fasta');

$seqobj = $seqio->next_seq();
$count = 5;
while ($count > 0){
         print $seqobj->seq();
         $seqobj = $seqio->next_seq();

}
-
Darin M. London
Bioinformatics Investigator
R & D - Bioinformatics Operations
GlaxoSmithKline
Internal
MAIN A1909.1f

External
5 Moore Drive
P.O. Box 13398
MAIN A1909.1f
Research Triangle Park
NC 27709
Phone: (919) 483 - 0710