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

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)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq