Bio::Search::Result::BlastPullResult.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   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::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)