/ 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Search::HSP::HmmpfamHSP

NAME

Bio::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:

https://github.com/bioperl/bioperl-live/issues

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