| Bio::Search::HSP::HmmpfamHSP(3pm) | User Contributed Perl Documentation | Bio::Search::HSP::HmmpfamHSP(3pm) |
Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.hmmer');
while (my $result = $in->next_result) {
while (my $hit = $result->next_hit) {
print $hit->name, "\n";
print $hit->score, "\n";
print $hit->significance, "\n";
while (my $hsp = $hit->next_hsp) {
# process HSPI objects
}
}
}
This object implements a parser for hmmpfam hsp output, a program in the HMMER package.
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Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
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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::HmmpfamHSP->new();
Function: Builds a new Bio::Search::HSP::HmmpfamHSP object.
Returns : Bio::Search::HSP::HmmpfamHSP
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
-hsp_data => array ref with [rank query_start query_end hit_start
hit_end score evalue]
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
hsp, and $start and $end define the tell() position within the
filehandle that the hsp data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : none
Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : [optional] new value to set
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gaps in the query, hit, or total alignment.
Returns : Integer, number of gaps or 0 if none
Args : 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP Returns : undef (Hmmpfam reports do not have p-values) Args : none
| 2018-10-27 | perl v5.26.2 |