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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, "\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:

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

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