[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