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

[Jason Eric Stajich]

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