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

Jack Chen chenn at cshl.edu
Thu Oct 14 22:33:24 EDT 2004

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




#!/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);

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";

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