[Bioperl-l] Bio::Search results

[Sean O'Keeffe]

Hi,
The following code snippet is something I use to extract information
from hmmer result files:

use Bio::SearchIO;

my $in = new Bio::SearchIO( -format => 'hmmer',  -file => $ARGV[0] );
while(my $result = $in->next_result) {
  print $result->query_name(), "\n",$result->query_description(),"\n";
  while (my $hit = $result->next_hit) {
    while(my $hsp = $hit->next_domain) {
      next unless ($hsp->name =~ /^ig|^lrr|^fn3|^egf|^tsp|^psi/i);
      print $hsp->start(),"\t",$hsp->end(),"\t",$hsp->evalue(),"\n";
    }
  }
}

The input file is generated by hmmpfam and is given at the command
line. I use it to scan for specific domain names e.g ig, fn3 lrr etc.
This code works for the first loop and then ends so I get the name and
description (no hsp values as their are none for this result):

ENSMUSP00000065602 
pep:novel supercontig::NT_085813:405:1510:-1 gene:ENSMUSG00000054059
transcript:ENSMUST00000066517

My question is why does the loop end after one instance. Incidentally
the outputted  name and description above are the last ones in the
hmmer file (maybe the file is read from the back? - don't know if this
means anything).
Any thoughts would be appreciated. Thanks,
Sean.