Bio::Search::HSP::BlastPullHSP man page on Fedora

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Bio::Search::HSP::BlasUserlContributed Perl DBio::Search::HSP::BlastPullHSP(3)

NAME
       Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN
       hsps

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

	   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 BlastN hsp 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:

	 http://bugzilla.open-bio.org/

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::BlastNHSP->new();
	Function: Builds a new Bio::Search::HSP::BlastNHSP object.
	Returns : Bio::Search::HSP::BlastNHSP
	Args	: -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
		  -parent => Bio::PullParserI object (required if no -chunk)

		  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 gap characters in the query, hit, or total alignment.
	Returns	 : Integer, number of gap characters 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'

   strand
	Title	: strand
	Usage	: $hsp->strand('query')
	Function: Retrieves the strand for the HSP component requested
	Returns : +1 or -1 (0 if unknown)
	Args	: 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
		  'query' to retrieve the query strand (default)
		  'list' or 'array' to retreive both query and hit together

   start
	Title	: start
	Usage	: $hsp->start('query')
	Function: Retrieves the start for the HSP component requested
	Returns : integer, or list of two integers (query start and subject start) in
		  list context
	Args	: 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject
		  'query' to retrieve the query start (default)

   end
	Title	: end
	Usage	: $hsp->end('query')
	Function: Retrieves the end for the HSP component requested
	Returns : integer, or list of two integers (query end and subject end) in
		  list context
	Args	: 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject
		  'query' to retrieve the query end (default)

   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

perl v5.14.1			  2011-07-22 Bio::Search::HSP::BlastPullHSP(3)
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