| Bio::Search::HSP::FastaHSP(3pm) | User Contributed Perl Documentation | Bio::Search::HSP::FastaHSP(3pm) |
Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data
# get a FastaHSP from a SearchIO stream
my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta');
while( my $r = $in->next_result) {
while( my $hit = $r->next_result ) {
while( my $hsp = $hit->next_hsp ) {
print "smith-waterman score (if available): ",
$hsp->sw_score(),"\n";
}
}
}
Describe the object here
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::Search::HSP::FastaHSP->new(); Function: Builds a new Bio::Search::HSP::FastaHSP object Returns : Bio::Search::HSP::FastaHSP Args : -swscore => smith-waterman score
Title : sw_score Usage : $obj->sw_score($newval) Function: Get/Set Smith-Waterman score Returns : value of sw_score Args : newvalue (optional)
Title : evalue2 Usage : $obj->evalue2($newval) Function: Get/Set E2() expectation value Returns : value of evalue2 Args : newvalue (optional)
| 2020-10-28 | perl v5.30.3 |