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Bio::Search::Result::HUseraContributed PeBio::Search::Result::HmmpfamResult(3)

NAME
       Bio::Search::Result::HmmpfamResult - A parser and result	object for
       hmmpfam
					    results

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) {
		       print $result->query_name, " ", $result->algorithm, " ",	$result->num_hits(), " hits\n";
	   }

DESCRIPTION
       This object implements a	parser for hmmpfam result 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::SearchIO::Result::hmmpfam->new();
	Function: Builds a new Bio::SearchIO::Result::hmmpfam object
	Returns	: Bio::SearchIO::Result::hmmpfam
	Args	: -chunk  => [Bio::Root::IO, $start, $end] (required if	no -parent)
		  -parent => Bio::PullParserI object (required if no -chunk)
		  -parameters => hash ref of search parameters (key => value), optional
		  -statistics => hash ref of search statistics (key => value), optional

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

   next_hit
	Title	: next_hit
	Usage	: while( $hit =	$result->next_hit()) { ... }
	Function: Returns the next available Hit object, representing potential
		  matches between the query and	various	entities from the database.
	Returns	: a Bio::Search::Hit::HitI object or undef if there are	no more.
	Args	: none

   next_model
	Title	: next_model
	Usage	: my $domain = $result->next_model
	Function: Returns the next domain - this is an alias for next_hit()
	Returns	: L<Bio::Search::Hit::HitI> object
	Args	: none

   hits
	Title	: hits
	Usage	: my @hits = $result->hits
	Function: Returns the HitI objects contained within this Result
	Returns	: Array	of Bio::Search::Hit::HitI objects
	Args	: none

       See Also: Bio::Search::Hit::HitI

   models
	Title	: models
	Usage	: my @domains =	$result->models;
	Function: Returns the list of HMM models seen -	this is	an alias for hits()
	Returns	: Array	of L<Bio::Search::Hit::HitI> objects
	Args	: none

   sort_hits
	Title	       : sort_hits
	Usage	       : $result->sort_hits('<score')
	Function       : Sorts the hits	so that	they come out in the desired order when
		     hits() or next_hit() is called.
	Returns	       : n/a
	Args	       : A coderef for the sort	function. See the documentation	on the Perl
		     sort() function for guidelines on writing sort functions.
				 You will be sorting array references, not HitI	objects. The
				 references contain name as element 0, description as element 1,
				 score as element 2, significance as element 3 and number of hsps
				 as element 4.
				 By default the	sort order is ascending	significance value (ie.
				 most significant hits first).
	Note	       : To access the special variables $a and	$b used	by the Perl sort()
		     function the user function	must access
				 Bio::Search::Result::HmmpfamResult namespace.
		     For example, use :
		     $result->sort_hits(
				       sub{$Bio::Search::Result::HmmpfamResult::a->[2]
								<=>
					       $Bio::Search::Result::HmmpfamResult::b->[2]});
		     NOT $result->sort_hits($a->[2] <=>	$b->[2]);

   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

perl v5.24.1			  2017-07Bio::Search::Result::HmmpfamResult(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sendu Bala | APPENDIX

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