NAME

Bio::Polloc::Rule::profile - A rule of type profile

AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

APPENDIX

Methods provided by the package

new

Generic initialization function

execute

Runs the search using HMMer

Arguments

The sequence (-seq) as a Bio::Seq object or a Bio::SeqIO object

Returns

An array reference populated with Bio::Polloc::Locus::repeat objects

stringify_value

Produces a readable string of the rule's value

INTERNAL METHODS

Methods intended to be used only within the scope of Bio::Polloc::*

_qualify_value

Implements the _qualify_value from the Bio::Polloc::RuleI interface

Arguments

Value (str or ref-to-hash or ref-to-array). Mandatory arguments are:

-hmm str

Path to the file containing the HMM.

See the documentation of HMMER for detailed description of the arguments mapped by the followin supported keys:

evalue

score

ince

inct

incdome

incdomt

f1

f2

f3

domz

seed

tformat

cpu

acc

cut_ga

cut_nc

cut_tc

max

noheuristics

nobias

nonull2

Return

Value (ref-to-hash or undef)

_initialize