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.

  [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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email [email protected]

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)