Hello,

I'd like to use the bioperl Bio::Tools::Est2Genome module to
parse some est2genome output files to make gff format parsed output, 
but am having some problems.

I'm using bioperl 1.5.1 and my perl script looks like this:

use Bio::Tools::Est2Genome; 
$est2genome  = Bio::Tools::Est2Genome->new(-file => $est2genome_file);
while(my $gene = $est2genome->parse_next_gene(1)) 
{
    foreach my $transcript($gene->transcripts)
    {
       @exons              = $transcript->exons;
       foreach my $exon(@exons)
       {
           $gff_string      = $exon->gff_string(); 
           print "$gff_string\n";
       }
    }
}
$est2genome->close();


When I run my perl script I get an error message saying:

> ------------- EXCEPTION  -------------
> MSG: Bio::SeqFeature::Gene::Exon=HASH(0x1409a54b0) is on opposite strand from Bio::SeqFeature::Gene::Transcript=HASH(0x1400223d0)
> STACK Bio::SeqFeature::Gene::Transcript::_add /nfs/disk100/wormpub2/Avril/downloadnov05/bioperl/bioperl-1.5.1//Bio/SeqFeature/Gene/Transcript.pm:734
> STACK Bio::SeqFeature::Gene::Transcript::add_exon /nfs/disk100/wormpub2/Avril/downloadnov05/bioperl/bioperl-1.5.1//Bio/SeqFeature/Gene/Transcript.pm:225
> STACK Bio::Tools::Est2Genome::_parse_gene_struct /nfs/disk100/wormpub2/Avril/downloadnov05/bioperl/bioperl-1.5.1//Bio/Tools/Est2Genome.pm:325
> STACK Bio::Tools::Est2Genome::parse_next_gene /nfs/disk100/wormpub2/Avril/downloadnov05/bioperl/bioperl-1.5.1//Bio/Tools/Est2Genome.pm:169
> STACK toplevel /nfs/team54/alc/perl/parse_est2genome_bioperl.pl:57


I've tried running my script on two different est2genome output files,
and get the same error. Do you know is this likely to be a problem with my script,
with the est2genome input file, or with the bioperl module? I will appreciate
any suggestions very much.

regards,
Avril Coghlan
Sanger Institute






