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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

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