[Bioperl-l] genbank to gff and vice versa

Marc Logghe Marc.Logghe at devgen.com
Mon Jun 21 10:46:11 EDT 2004


> Is the reverse flow possible?
> 
Only if you have your (fasta) sequence sitting somewhere you can turn a GFF line into a feature and add it.
my $seq = $fasta->next_seq;
my @feat;
while (<GFF>)
{
  chomp;
  next if /^$/;
  puch @feat, Bio::SeqFeature::Generic->new( -gff_string => $_ );
}
$seq->add_SeqFeature(@feat);

or something alike.

HTH,
Marc




***********************************************************
Marc Logghe, Ph.D.
Senior Scientist
Scientific Computing Group
Devgen nv
Technologiepark 9
B - 9052 Ghent-Zwijnaarde
Belgium
Tel: +32 9 324 24 88
Fax: +32 9 324 24 25

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