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src/c/o/cogent-1.5.3/cogent/evolve/models.py   cogent(Download)
import numpy
from cogent.evolve import substitution_model
from cogent.evolve.predicate import MotifChange, replacement
from cogent.evolve.solved_models import F81, HKY85, TN93
 
 
# Substitution model rate matrix predicates
_gtr_preds = [MotifChange(x,y) for x,y in ['AC', 'AG', 'AT', 'CG', 'CT']]
_kappa = (~MotifChange('R','Y')).aliased('kappa')
_omega = replacement.aliased('omega')

src/p/y/pycogent-HEAD/cogent/evolve/models.py   pycogent(Download)
import numpy
from cogent.evolve import substitution_model
from cogent.evolve.predicate import MotifChange, replacement
from cogent.evolve.solved_models import F81, HKY85, TN93
 
 
# Substitution model rate matrix predicates
_gtr_preds = [MotifChange(x,y) for x,y in ['AC', 'AG', 'AT', 'CG', 'CT']]
_kappa = (~MotifChange('R','Y')).aliased('kappa')
_omega = replacement.aliased('omega')

src/c/o/cogent-1.5.3/cogent/evolve/solved_models.py   cogent(Download)
 
from cogent.evolve.substitution_model import Nucleotide, CalcDefn
from cogent.evolve.predicate import MotifChange
from cogent.maths.matrix_exponentiation import FastExponentiator
import numpy

src/p/y/pycogent-HEAD/cogent/evolve/solved_models.py   pycogent(Download)
 
from cogent.evolve.substitution_model import Nucleotide, CalcDefn
from cogent.evolve.predicate import MotifChange
from cogent.maths.matrix_exponentiation import FastExponentiator
import numpy

src/c/o/cogent-1.5.3/tests/test_evolve/test_newq.py   cogent(Download)
                                                GeneralStationary
from cogent.evolve.discrete_markov import DiscreteSubstitutionModel
from cogent.evolve.predicate import MotifChange
from cogent.util.unit_test import TestCase, main
from cogent.maths.matrix_exponentiation import PadeExponentiator as expm
    def fit_constructed_gen(results=results):
        if 'constructed_gen' in results:
            return
        preds = [MotifChange(a,b, forward_only=True) for a,b in [['A', 'C'],
                        ['A', 'G'], ['A', 'T'], ['C', 'A'], ['C', 'G'],

src/p/y/pycogent-HEAD/tests/test_evolve/test_newq.py   pycogent(Download)
                                                GeneralStationary
from cogent.evolve.discrete_markov import DiscreteSubstitutionModel
from cogent.evolve.predicate import MotifChange
from cogent.util.unit_test import TestCase, main
from cogent.maths.matrix_exponentiation import PadeExponentiator as expm
    def fit_constructed_gen(results=results):
        if 'constructed_gen' in results:
            return
        preds = [MotifChange(a,b, forward_only=True) for a,b in [['A', 'C'],
                        ['A', 'G'], ['A', 'T'], ['C', 'A'], ['C', 'G'],

src/c/o/cogent-1.5.3/tests/test_evolve/test_scale_rules.py   cogent(Download)
    return  (x == 'A' and y == 'C') or (x == 'C' and y == 'A')
 
from cogent.evolve.predicate import MotifChange, replacement
 
__author__ = "Peter Maxwell and Gavin Huttley"
__status__ = "Production"
 
a_c = MotifChange('A', 'C')
trans = MotifChange('A', 'G') | MotifChange('T', 'C')
 

src/p/y/pycogent-HEAD/tests/test_evolve/test_scale_rules.py   pycogent(Download)
    return  (x == 'A' and y == 'C') or (x == 'C' and y == 'A')
 
from cogent.evolve.predicate import MotifChange, replacement
 
__author__ = "Peter Maxwell and Gavin Huttley"
__status__ = "Production"
 
a_c = MotifChange('A', 'C')
trans = MotifChange('A', 'G') | MotifChange('T', 'C')
 

src/p/y/pycogent-HEAD/tests/test_evolve/test_motifchange.py   pycogent(Download)
#!/usr/bin/env python
 
import unittest
from cogent.evolve.predicate import MotifChange
from cogent.core.moltype import CodonAlphabet
    def _makeMotifChange(self, *args, **kw):
        pred = MotifChange(*args, **kw)
        return pred.interpret(self.model)
 
    def assertMatch(self, pred, seq1, seq2):

src/c/o/cogent-1.5.3/tests/test_evolve/test_motifchange.py   cogent(Download)
#!/usr/bin/env python
 
import unittest
from cogent.evolve.predicate import MotifChange
from cogent.core.moltype import CodonAlphabet
    def _makeMotifChange(self, *args, **kw):
        pred = MotifChange(*args, **kw)
        return pred.interpret(self.model)
 
    def assertMatch(self, pred, seq1, seq2):