Bio::Tools::HMMER::Results - Object representing HMMER output results # parse a hmmsearch file (can also parse a hmmpfam file) $res = new Bio::Tools::HMMER::Results( -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"; } 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. Ewan then converted them to bioperl objects in 1999. That conversion is meant to be backwardly compatible, but may not be (caveat emptor).

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://www.bioperl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://www.bugzilla.bioperl.org/ Email birney@ebi.ac.uk Jason Stajich, jason@bioperl.org 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)