Bio::Search::Result::HmmpfamResult(3) A parser and result object for hmmpfam

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. 

  [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]

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

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