[Bioperl-l] problems with the Bio::Tools::Run::Genewise module

[Jack Chen]

Hi, Keith, Jason et al., 
 
I need you help with this module. I am trying to run genewise and parse
genewise result using the module. The simple script I wrote did not work
as expected. While I could get the exon coordinates correctly, I could not
retrieve sequence data properly, ie, transcript() does not return a
sequence.

When I ran the program on command line, I could get correct sequences. 

Any insight is appreciated.
 
Jack
 
============
 
> #!/usr/bin/perl -w
> use strict;
> use Getopt::Long;
> use Bio::SeqIO;
> use Bio::Tools::Run::Genewise;
> use Data::Dumper;
> 
> my ($hmmfile, $gen);
> GetOptions('hmm|h:s'    => \$hmmfile,
>            'genomic|g:s'=> \$gen);
> 
> my $genomic_seq = Bio::SeqIO->new(-file => $gen, -format => 'FASTA');
> my $factory = Bio::Tools::Run::Genewise->new('both' => 1, 'silent' => 1);
> 
> $factory->hmmer(1);
> my @genes = $factory->run($hmmfile, $genomic_seq->next_seq);
> 
> for my $g (@genes){
>   my @transcripts = $g->transcripts();
>   for my $tran (@transcripts){
>     print $tran->cds, "\n";
>   }
> }