Bio::Search::Hit::BlastPullHit(3pm)			User Contributed Perl Documentation		       Bio::Search::Hit::BlastPullHit(3pm)

NAME

       Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits

SYNOPSIS

	   # generally we use Bio::SearchIO to build these objects
	   use Bio::SearchIO;
	   my $in = Bio::SearchIO->new(-format => 'blast_pull',
								  -file   => 'result.blast');

	   while (my $result = $in->next_result) {
		       while (my $hit = $result->next_hit) {
			       print $hit->name, "
";
			       print $hit->score, "
";
			       print $hit->significance, "
";

			       while (my $hsp = $hit->next_hsp) {
				       # process HSPI objects
			       }
		       }
	   }

DESCRIPTION

       This object implements a parser for BLASTN hit output.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

CONTRIBUTORS

       Additional contributors names and emails here

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::BlastNHit->new();
	Function: Builds a new Bio::Search::Hit::BlastNHit object.
	Returns : Bio::Search::Hit::BlastNHit
	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]

		  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

   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

   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 HSP iterator to the beginning, so that
		  next_hsp() will subsequently return the first hsp and so on.
	Returns : n/a
	Args	: none

perl v5.14.2							    2012-03-02				       Bio::Search::Hit::BlastPullHit(3pm)