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FAST-1.06
River stage zero No dependents
/ FAST::Bio::Search::Result::HmmpfamResult

NAME

FAST::Bio::Search::Result::HmmpfamResult - A parser and result object for hmmpfam results

SYNOPSIS


            

              
              
  # generally we use FAST::Bio::SearchIO to build these objects
  use FAST::Bio::SearchIO;
  my $in = FAST::Bio::SearchIO->new(-format => 'hmmer_pull',
                                           -file   => 'result.hmmer');
  while (my $result = $in->next_result) {
print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
  }

DESCRIPTION

This object implements a parser for hmmpfam result output, a program in the HMMER package.

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

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 = FAST::Bio::SearchIO::Result::hmmpfam->new();
Function: Builds a new FAST::Bio::SearchIO::Result::hmmpfam object 
Returns : FAST::Bio::SearchIO::Result::hmmpfam
Args    : -chunk  => [FAST::Bio::Root::IO, $start, $end] (required if no -parent)
          -parent => FAST::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 FAST::Bio::Search::Hit::HitI object or undef if there are no more.
Args    : none

next_model


            

              
              
Title   : next_model
Usage   : my $domain = $result->next_model
Function: Returns the next domain - this is an alias for next_hit()
Returns : L<FAST::Bio::Search::Hit::HitI> object
Args    : none

hits


            

              
              
Title   : hits
Usage   : my @hits = $result->hits
Function: Returns the HitI objects contained within this Result
Returns : Array of FAST::Bio::Search::Hit::HitI objects
Args    : none

See Also: FAST::Bio::Search::Hit::HitI

models


            

              
              
Title   : models
Usage   : my @domains = $result->models;
Function: Returns the list of HMM models seen - this is an alias for hits()
Returns : Array of L<FAST::Bio::Search::Hit::HitI> objects
Args    : none

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.
                  You will be sorting array references, not HitI objects. The
                  references contain name as element 0, description as element 1,
                  score as element 2, significance as element 3 and number of hsps
                  as element 4.
                  By default the sort order is ascending significance value (ie.
                  most significant hits first).
Note            : To access the special variables $a and $b used by the Perl sort()
             function the user function must access
                  FAST::Bio::Search::Result::HmmpfamResult namespace. 
             For example, use : 
             $result->sort_hits(
                        sub{$FAST::Bio::Search::Result::HmmpfamResult::a->[2]
                                                 <=> 
                                $FAST::Bio::Search::Result::HmmpfamResult::b->[2]});
             NOT $result->sort_hits($a->[2] <=> $b->[2]);

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