Bio::Search::Result::HmmpfamResult.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

     # generally we use Bio::SearchIO to build these objects
     use Bio::SearchIO;
     my $in = 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:
   http://bugzilla.open-bio.org/
 
 

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 = 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
 
 

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<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 Bio::Search::Hit::HitI objects
  Args    : none
 
 

See Also: 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<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
                           Bio::Search::Result::HmmpfamResult namespace. 
               For example, use : 
               $result->sort_hits(
                                 sub{$Bio::Search::Result::HmmpfamResult::a->[2]
                                                          <=> 
                                         $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