Provided by: libbio-perl-perl_1.6.901-2_all bug

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, "\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 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