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

Vladimir Babenko bob@SNOWBALL.PCBI.upenn.edu
Sat, 22 Sep 2001 13:19:22 -0700


   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