[Bioperl-l] my life with fuzzy

[Jason Stajich]

Taking a cue from biojava folks I am running parses on complete genbank
dbs.  Right now looking at primate db.  The fixes implemented last week
seem to allow all seqs to run through fine.

Anyone want to volunteer to run through the EMBL db if you have it local
EMBL db copy?

I am simply running this very basic script (obviously one would change
format to EMBL when running on EMBL db):

#!/usr/local/bin/perl -w
use strict;

use Bio::SeqIO;
# get filename from cmdline
open(GBPRI, shift) or die;
my $count = 0;
while(<GBPRI>) {
    last if ( $count++ >= 7);
}

my $seqio = new Bio::SeqIO(-format => 'genbank',
			   -fh   => \*GBPRI);
$count =0;
while( my $seq = $seqio->next_seq ) {
    if( $count > 0 && $count % 100 == 0 ) { print $count, " seqs
processed\n";}
    $count++;
}
print $count, " seqs processed\n";

__END__

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/