[Bioperl-l] Features: parsing the join(x1..x2,x3,..x4)

[Vladimir Babenko]

  Hi,
  the answer is:
# $Id: FTHelper.pm,v 1.25 2001/02/27 23:18:11 jason Exp $
  and I'm using Bioperl 0.7.0
    Thanks,
   -Vladimir
Jason Eric Stajich wrote:

> please do
> % perldoc -m Bio::SeqIO::FTHelper | grep Id
> so we can see which version of the feature table parsing module you are
> using.
>
> Would be good to report which version of bioperl you have installed as
> well.
>
> -Jason
> On Sat, 22 Sep 2001, Vladimir Babenko wrote:
>
> >    Hi,
> > I want to splice the mRNA out of the genomic sequence.
> > I'm experiencing the problem parsing the join from EMBL FT, for example
> > the string:
> > FT   mRNA   join(501..646,992..1048,1157..1216,1492..1564)
> >
> > I'm using the code:
> >
> > use Bio::Seq;
> > use Bio::SeqIO;
> > my $embl_file = $ARGV[0];
> > my $in = Bio::SeqIO->new(-file => $embl_file,-format => 'EMBL');
> > while (defined($seq = $in->next_seq())) {
> >   foreach my $feature (my $seq->top_SeqFeatures) {
> > my @exons = $feature->sub_SeqFeature();
> > print scalar(@exons)."\n";
> > }
> > }
> > which returns 0 while parsing the string above.
> > Maybe my Bioperl lib is not complete?
> >    Thanks a lot,
> >        Vladimir
> >
> >
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> >
>
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu