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

[Jason Eric Stajich]

I think we have fixed the problems you are experiencing since that
release. I would suggest upgrading to bioperl 0.7.1 and giving it another
try.

You can download it from CPAN or
ftp://bioperl.org/pub/DIST/bioperl-0.7.1.tar.gz

-jason

On Sat, 22 Sep 2001, Vladimir Babenko wrote:

>   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
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
>
>
>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu