Bio::Tools::HMMER::Results(3pm) User Contributed Perl Documentation 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,"
";
foreach $domain ( $seq->each_Domain ) {
print " Domain start ",$domain->start," end ",$domain->end,
" score ",$domain->bits,"
";
}
}
# 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,"
";
}
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
";
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)
perl v5.14.2 2012-03-02 Bio::Tools::HMMER::Results(3pm)