[Bioperl-l] sim4 to GFF

[Charles Hauser]

All,

Attempting to parse sim4 data, and have not figured out to process a
multi-report file.  I know I am staring right at it, but the brain cells
are tired.

my $sim4 = Bio::Tools::Sim4::Results->new(-file => $filename,
					  -estfirst => 0);

This code process the 1st report only.

I need another while( ->next_report) loop?


while(my $exonset = $sim4->next_exonset()) {
    print "Delimited on sequence ", $exonset->seq_id(), 
             "from ", $exonset->start(), " to ", $exonset->end(), "\n";
    foreach my $exon ( $exonset->sub_SeqFeature() ) {
	print "Exon from ", $exon->start, " to ", $exon->end, 
                " on strand ", $exon->strand(), "\n";
	my $homol = $exon->est_hit();
	print "Matched to sequence ", $homol->seq_id, 
                " at ", $homol->start," to ", $homol->end, "\n";
    }
}


Charles