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Bio::Search::Result::BUserPContributed)Bio::Search::Result::BlastPullResult(3)

NAME
       Bio::Search::Result::BlastPullResult - A	parser and result object for
       BLASTN
					    results

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

DESCRIPTION
       This object implements a	parser for NCBI	BLASTN result 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://github.com/bioperl/bioperl-live/issues

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::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

   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

   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.
				 By default the	sort order is ascending	significance value (ie.
				 most significant hits first).
				 *** example

   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

   get_statistic
	Title	: get_statistic
	Usage	: my $gap_ext =	$result->get_statistic('kappa')
	Function: Returns the value for	a specific statistic available
		  from this result
	Returns	: string
	Args	: name of statistic (string)

   get_parameter
	Title	: get_parameter
	Usage	: my $gap_ext =	$result->get_parameter('gapext')
	Function: Returns the value for	a specific parameter used
		  when running this result
	Returns	: string
	Args	: name of parameter (string)

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

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

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