Package csb :: Package bio :: Package hmm :: Module pseudocounts :: Class PseudocountBuilder

Class PseudocountBuilder

object --+
         |
        PseudocountBuilder

Constructs profile HMMs with pseudocounts.

Instance Methods

__init__(self, hmm)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

add_emission_pseudocounts(self, tau=0.1, pca=2.5, pcb=0.5, pcc=1.0)
Port from HHpred, it uses the conditional background probabilities, inferred from the Gonnet matrix.

source code

add_transition_pseudocounts(self, gapb=1.0, gapd=0.15, gape=1.0, gapf=0.6, gapg=0.6, gapi=0.6)
Add pseudocounts to the transitions.

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties
	hmm
Inherited from `object`: `__class__`

Method Details

init(self, hmm)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

add_emission_pseudocounts(self, tau=0.1, pca=2.5, pcb=0.5, pcc=1.0)

source code

Port from HHpred, it uses the conditional background probabilities, inferred from the Gonnet matrix.

Parameters:

tau (float) - admission weight, i.e how much of the final score is determined by the background probabilities. 0.0=no pseudocounts.

add_transition_pseudocounts(self, gapb=1.0, gapd=0.15, gape=1.0, gapf=0.6, gapg=0.6, gapi=0.6)

source code

Add pseudocounts to the transitions. A port from hhsearch -gapb 1.0 -gapd 0.15 -gape 1.0 -gapf 0.6 -gapg 0.6 -gapi 0.6

Property Details

hmm

Get Method:: unreachable.hmm(self)

Class PseudocountBuilder

__init__(self, hmm) (Constructor)

add_emission_pseudocounts(self, tau=0.1, pca=2.5, pcb=0.5, pcc=1.0)

add_transition_pseudocounts(self, gapb=1.0, gapd=0.15, gape=1.0, gapf=0.6, gapg=0.6, gapi=0.6)

hmm

init(self, hmm)
(Constructor)