NAME

Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits

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 hit 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::Hit::HmmpfamHit->new();
 Function: Builds a new Bio::Search::Hit::HmmpfamHit object.
 Returns : Bio::Search::Hit::HmmpfamHit
 Args    : -chunk    => [Bio::Root::IO, $start, $end] (required if no -parent)
           -parent   => Bio::PullParserI object (required if no -chunk)
           -hit_data => array ref with [name description score significance
		                                num_hsps rank]

           where the array ref provided to -chunk contains an IO object
           for a filehandle to something representing the raw data of the
           hit, and $start and $end define the tell() position within the
           filehandle that the hit data starts and ends (optional; defaults
           to start and end of the entire thing described by the filehandle)

next_hsp

Title    : next_hsp
Usage    : while( $hsp = $obj->next_hsp()) { ... }
Function : Returns the next available High Scoring Pair
Example  : 
Returns  : L<Bio::Search::HSP::HSPI> object or null if finished
Args     : none

next_domain

Title   : next_domain 
Usage   : my $domain = $hit->next_domain();
Function: An alias for L<next_hsp()>, this will return the next HSP
Returns : L<Bio::Search::HSP::HSPI> object
Args    : none

hsps

Usage     : $hit_object->hsps();
Purpose   : Get a list containing all HSP objects.
Example   : @hsps = $hit_object->hsps();
Returns   : list of L<Bio::Search::HSP::BlastHSP> objects.
Argument  : none

domains

Title   : domains
Usage   : my @domains = $hit->domains();
Function: An alias for L<hsps()>, this will return the full list of hsps
Returns : array of L<Bio::Search::HSP::HSPI> objects
Args    : none

hsp

Usage     : $hit_object->hsp( [string] );
Purpose   : Get a single HSPI object for the present HitI object.
Example   : $hspObj  = $hit_object->hsp;  # same as 'best'
          : $hspObj  = $hit_object->hsp('best');
          : $hspObj  = $hit_object->hsp('worst');
Returns   : Object reference for a L<Bio::Search::HSP::HSPI> object.
Argument  : String (or no argument).
          :   No argument (default) = highest scoring HSP (same as 'best').
          :   'best'  = highest scoring HSP.
          :   'worst' = lowest scoring HSP.
Throws    : Exception if an unrecognized argument is used.

See Also : hsps(), num_hsps()

rewind

Title   : rewind
Usage   : $result->rewind;
Function: Allow one to reset the Hit iterator to the beginning, so that
          next_hit() will subsequently return the first hit and so on.
Returns : n/a
Args    : none

strand

 Usage     : $sbjct->strand( [seq_type] );
 Purpose   : Gets the strand(s) for the query, sbjct, or both sequences.
           : For hmmpfam, the answers are always 1 (forward strand).
 Example   : $qstrand = $sbjct->strand('query');
           : $sstrand = $sbjct->strand('hit');
           : ($qstrand, $sstrand) = $sbjct->strand();
 Returns   : scalar context: integer '1'
           : array context without args: list of two strings (1, 1)
           : Array context can be "induced" by providing an argument of 'list'
		   : or 'array'.
 Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default
           : = 'query') ('sbjct' is synonymous with 'hit')

frac_aligned_query

Usage     : $hit_object->frac_aligned_query();
Purpose   : Get the fraction of the query sequence which has been aligned
          : across all HSPs (not including intervals between non-overlapping
          : HSPs).
Example   : $frac_alnq = $hit_object->frac_aligned_query();
Returns   : undef (the length of query sequences is unknown in Hmmpfam reports)
Argument  : none

cpanm Bio::SearchIO::hmmer

perl -MCPAN -e shell
install Bio::SearchIO::hmmer