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use Bio::SearchIO;
use Data::Dumper;
my $sHMMFilename = 'new.hmm';
# Open HMMer-Report
my $oHMMReport = Bio::SearchIO->new ('-file' => $sHMMFilename,
'-format' => 'hmmer');
# Cycle through results
while (my $oHMMResult=$oHMMReport->next_result) {
print "processing ", Dumper(\$oHMMResult) ,"\n";
while (my $oHMMerHit=$oHMMResult->next_hit) {
print "processing $oHMMerHit\n";
while (my $oHMMerHsp=$oHMMerHit->next_hsp) {
print "processing $oHMMerHsp\n";
# Skip hit if it has a too high E-value or too low score
if (($oHMMerHsp->evalue > $fEvalue) or
($oHMMerHsp->score < $fScore)) {
if ($bVerbose) {
print "processing $sHMMFilename\n";
print "done.\n";
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