Bio::Search::HSP::HmmpUserSContributed Perl DocBio::Search::HSP::HmmpfamHSP(3)NAMEBio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps
SYNOPSIS
# 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
}
}
}
DESCRIPTION
This object implements a parser for hmmpfam hsp output, a program in
the HMMER package.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
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)
query
Title : query
Usage : my $query = $hsp->query
Function: Returns a SeqFeature representing the query in the HSP
Returns : L<Bio::SeqFeature::Similarity>
Args : none
hit
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
gaps
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'
pvalue
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
perl v5.14.1 2011-07-22 Bio::Search::HSP::HmmpfamHSP(3)
