Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Tools::HMMER::Results - Object representing HMMER output results

SYNOPSIS

          # parse a hmmsearch file (can also parse a hmmpfam file)
          $res = Bio::Tools::HMMER::Results->new( -file => 'output.hmm' ,
                                                 -type => 'hmmsearch');

          # print out the results for each sequence
          foreach $seq ( $res->each_Set ) {
              print "Sequence bit score is",$seq->bits,"\n";
              foreach $domain ( $seq->each_Domain ) {
                  print " Domain start ",$domain->start," end ",$domain->end,
                  " score ",$domain->bits,"\n";
              }
          }

          # new result object on a sequence/domain cutoff of
          # 25 bits sequence, 15 bits domain
          $newresult = $res->filter_on_cutoff(25,15);

          # alternative way of getting out all domains directly
          foreach $domain ( $res->each_Domain ) {
              print "Domain on ",$domain->seq_id," with score ",
              $domain->bits," evalue ",$domain->evalue,"\n";
          }

DESCRIPTION

       This object represents HMMER output, either from hmmsearch or hmmpfam. For hmmsearch, a
       series of HMMER::Set objects are made, one for each sequence, which have the the bits
       score for the object. For hmmpfam searches, only one Set object is made.

       These objects come from the original HMMResults modules used internally in Pfam, written
       by Ewan Birney. Ewan then converted them to BioPerl objects in 1999. That conversion is
       meant to be backwardly compatible, but may not be (caveat emptor).

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 one of the Bioperl mailing lists.  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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney

       Email birney@ebi.ac.uk

CONTRIBUTORS

       Jason Stajich, jason-at-bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   next_feature
        Title   : next_feature
        Usage   : while( my $feat = $res->next_feature ) { # do something }
        Function: SeqAnalysisParserI implementing function
        Example :
        Returns : A Bio::SeqFeatureI compliant object, in this case,
                  each DomainUnit object, ie, flattening the Sequence
                  aspect of this.
        Args    : None

   number
        Title   : number
        Usage   : print "There are ",$res->number," domains hit\n";
        Function: provides the number of domains in the HMMER report

   seqfile
        Title   : seqfile
        Usage   : $obj->seqfile($newval)
        Function:
        Example :
        Returns : value of seqfile
        Args    : newvalue (optional)

   hmmfile
        Title   : hmmfile
        Usage   : $obj->hmmfile($newval)
        Function:
        Example :
        Returns : value of hmmfile
        Args    : newvalue (optional)

   add_Domain
        Title   : add_Domain
        Usage   : $res->add_Domain($unit)
        Function: adds a domain to the results array. Mainly used internally.
        Args    : A Bio::Tools::HMMER::Domain

   each_Domain
        Title   : each_Domain
        Usage   : foreach $domain ( $res->each_Domain() )
        Function: array of Domain units which are held in this report
        Returns : array
        Args    : none

   domain_bits_cutoff_from_evalue
        Title   : domain_bits_cutoff_from_evalue
        Usage   : $cutoff = domain_bits_cutoff_from_evalue(0.01);
        Function: return a bits cutoff from an evalue using the
                  scores here. Somewhat interesting logic:
                   Find the two bit score which straddle the evalue
                   if( 25 is between these two points) return 25
                   else return the midpoint.

                  This logic tries to ensure that with large signal to
                  noise separation one still has sensible 25 bit cutoff
        Returns :
        Args    :

   write_FT_output
        Title   : write_FT_output
        Usage   : $res->write_FT_output(\*STDOUT,'DOMAIN')
        Function: writes feature table output ala swissprot
        Returns :
        Args    :

   filter_on_cutoff
        Title   : filter_on_cutoff
        Usage   : $newresults = $results->filter_on_cutoff(25,15);
        Function: Produces a new HMMER::Results module which has
                  been trimmed at the cutoff.
        Returns : a Bio::Tools::HMMER::Results module
        Args    : sequence cutoff and domain cutoff. in bits score
                  if you want one cutoff, simply use same number both places

   write_ascii_out
        Title   : write_ascii_out
        Usage   : $res->write_ascii_out(\*STDOUT)
        Function: writes as
                  seq seq_start seq_end model-acc model_start model_end model_name
        Returns :
        Args    :

         FIXME: Now that we have no modelacc, this is probably a bad thing.

   write_GDF_bits
        Title   : write_GDF_bits
        Usage   : $res->write_GDF_bits(25,15,\*STDOUT)
        Function: writes GDF format with a sequence,domain threshold
        Returns :
        Args    :

   add_Set
        Title   : add_Set
        Usage   : Mainly internal function
        Function:
        Returns :
        Args    :

   each_Set
        Title   : each_Set
        Usage   :
        Function:
        Returns :
        Args    :

   get_Set
        Title   : get_Set
        Usage   : $set = $res->get_Set('sequence-name');
        Function: returns the Set for a particular sequence
        Returns : a HMMER::Set object
        Args    : name of the sequence

   _parse_hmmpfam
        Title   : _parse_hmmpfam
        Usage   : $res->_parse_hmmpfam($filehandle)
        Function:
        Returns :
        Args    :

   _parse_hmmsearch
        Title   : _parse_hmmsearch
        Usage   : $res->_parse_hmmsearch($filehandle)
        Function:
        Returns :
        Args    :

   parsetype
        Title   : parsetype
        Usage   : $obj->parsetype($newval)
        Function:
        Returns : value of parsetype
        Args    : newvalue (optional)