[Bioperl-l] Question about Fgenesh.pm

[Andrew Nunberg]

Hi,
I am trying to parse an fgenesh analysis file using Bio::Tools::Fgenesh from
bioperl-live

I  had to make a change in the module at line 320
from:
    $predobj->primary_tag($ExonTags{$flds[3]} . 'Exon');

to:
    $predobj->primary_tag($ExonTags{$flds[4]} . 'Exon');

For the parser to work.

I then wish to retreive the name of the dna sequence that was fed to the
parser using the analysis_subject/query method

$fgenesh = Bio::Tools::Fgenesh->new(-file=>"results file");
$gene = $fgenesh->next_prediction;

$fgenesh->analysis_subject;

This method returns undef, although it appears in the code that the info is
stored there.
Lines 366-373 from Fgenesh.pm
if(/^(FGENESH)\s+([\d\.]+)/) {
        $self->analysis_method($1);
        $self->analysis_method_version($2);
            if (/\s(\S+)\sgenomic DNA/) {
              $self->analysis_subject($1);
            }
        next;
    }
Any input would be appreciated
-- 
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com