[Bioperl-l] parsing sim4 results

[Brian Osborne]

Charles,

This is from the bptutorial:

use Bio::Tools::Sim4::Results;
  $sim4 = new Bio::Tools::Sim4::Results(-file => 't/data/sim4.rev',
                                        -estisfirst => 0);
  # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Sim4::Exons
  # as sub features
  $exonset = $sim4->next_exonset;
  @exons = $exonset->sub_SeqFeature();
  # $exon is-a Bio::SeqFeature::FeaturePair
  $exon = 1;
  $exonstart = $exons[$exon]->start();
  $estname = $exons[$exon]->est_hit()->seqname();
  $sim4->close();


Brian O.


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Charles Hauser
Sent: Friday, March 14, 2003 3:03 PM
To: BioPerl-List
Subject: [Bioperl-l] parsing sim4 results

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";
    }
}





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