[Bioperl-l] parsing sim4 results

[Charles Hauser]

All,

I'm trying to parse output from sim4 w/ script below.
Looking at docs, Bio::Tools::Sim4 has exon & results modules.

I get the error:Can't locate Bio/Tools/Sim4.pm in @INC, which of course
because there is no Sim4.pm.

Suggestions?

Charles


use strict;
use Bio::Tools::Sim4;

my $filename = shift @ARGV; 

if( $filename =~ /\.gz/ ) {
    open(FH, "zcat $filename |") || die("cannot run zcat on $filename:
$!");
} else {
    open(FH, $filename) || die("cannot open $filename: $!");
}
print STDERR "Processing: ",$filename, "\n";

my $sim4 = Bio::Tools::Sim4->new( -fh   => \*FH );


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";
    }
}