Luis M Rodríguez-R > Polloc-1.5.3b > Bio::Polloc::Rule::profile

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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

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