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Bio::Tools::HMMER::Results.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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)