[Bioperl-l] scf writing issues

Marc Logghe Marc.Logghe at devgen.com
Wed Dec 22 18:38:30 EST 2004

Hi all,
it seems there is a problem (at least I have ;-) when creating scf output starting from a
Bio::Seq::SeqWithQuality file. I used the following test script:

use Bio::SeqIO;
use Bio::Seq::SeqWithQuality;

my $scff = 'test.scf';

my $out = Bio::SeqIO->new( -file => ">$scff", -format => 'scf');
my $qs = Bio::Seq::SeqWithQuality->new
                       ( -qual => '10 20 30 40 50 50 20 10',
                         -seq => 'ATCGATCG',
                         -id  => 'human_id',
                         -accession_number => 'AL000012',

$out->write_seq(-target => $qs);

When you open the produced test.scf file in trev for instance, the sequence is
rubbish. It makes no difference when you pass the version paramater or not.

Has anybody else noticed these kind of issues with Bio::SeqIO::scf ?
I am using bioperl-release-1-4-0 but also tried my luck with bioperl-release-1-5-0-rc1.


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