Did I find the right examples for you? yes no

All Samples(16)  |  Call(14)  |  Derive(0)  |  Import(2)

src/c/o/cogent-1.5.3/tests/test_evolve/test_likelihood_function.py   cogent(Download)
    def test_dinucleotide(self):
        """test a dinucleotide model."""
        submod = substitution_model.Dinucleotide(
                equal_motif_probs=True,
                do_scaling=False,
    def test_simulateAlignment2(self):
        "Simulate alignment with dinucleotide model"
        al = LoadSeqs(data={'a':'ggaatt','c':'cctaat'})
        t = LoadTree(treestring="(a,c);")
        sm = substitution_model.Dinucleotide(mprob_model='tuple')
        def use_root_seq(root_sequence):
            al = LoadSeqs(data={'a':'ggaatt','c':'cctaat'})
            t = LoadTree(treestring="(a,c);")
            sm = substitution_model.Dinucleotide(mprob_model='tuple')
            lf = sm.makeParamController(t)

src/p/y/pycogent-HEAD/tests/test_evolve/test_likelihood_function.py   pycogent(Download)
    def test_dinucleotide(self):
        """test a dinucleotide model."""
        submod = substitution_model.Dinucleotide(
                equal_motif_probs=True,
                do_scaling=False,
    def test_simulateAlignment2(self):
        "Simulate alignment with dinucleotide model"
        al = LoadSeqs(data={'a':'ggaatt','c':'cctaat'})
        t = LoadTree(treestring="(a,c);")
        sm = substitution_model.Dinucleotide(mprob_model='tuple')
        def use_root_seq(root_sequence):
            al = LoadSeqs(data={'a':'ggaatt','c':'cctaat'})
            t = LoadTree(treestring="(a,c);")
            sm = substitution_model.Dinucleotide(mprob_model='tuple')
            lf = sm.makeParamController(t)

src/c/o/cogent-1.5.3/tests/test_evolve/test_parameter_controller.py   cogent(Download)
    def test_pairwise_clock(self):
        al = LoadSeqs(data={'a':'agct','b':'ggct'})
        tree = LoadTree(treestring='(a,b);')
        model = cogent.evolve.substitution_model.Dinucleotide(
                do_scaling=True, equal_motif_probs=True, model_gaps=True,

src/p/y/pycogent-HEAD/tests/test_evolve/test_parameter_controller.py   pycogent(Download)
    def test_pairwise_clock(self):
        al = LoadSeqs(data={'a':'agct','b':'ggct'})
        tree = LoadTree(treestring='(a,b);')
        model = cogent.evolve.substitution_model.Dinucleotide(
                do_scaling=True, equal_motif_probs=True, model_gaps=True,

src/c/o/cogent-1.5.3/tests/test_evolve/test_substitution_model.py   cogent(Download)
    def setUp(self):
        self.submodel = substitution_model.Dinucleotide(do_scaling=True, 
                model_gaps=True, mprob_model='tuple')
 
    def test_asciiArt(self):
        model = substitution_model.Dinucleotide(mprob_model='tuple', 
            predicates=['k:transition'])    
        model.asciiArt()
        model = substitution_model.Dinucleotide(mprob_model='tuple')

src/p/y/pycogent-HEAD/tests/test_evolve/test_substitution_model.py   pycogent(Download)
    def setUp(self):
        self.submodel = substitution_model.Dinucleotide(do_scaling=True, 
                model_gaps=True, mprob_model='tuple')
 
    def test_asciiArt(self):
        model = substitution_model.Dinucleotide(mprob_model='tuple', 
            predicates=['k:transition'])    
        model.asciiArt()
        model = substitution_model.Dinucleotide(mprob_model='tuple')

src/p/y/pycogent-HEAD/tests/benchmark.py   pycogent(Download)
#!/usr/bin/env python
 
import sys #,hotshot
 
from cogent.evolve.substitution_model import Nucleotide, Dinucleotide, Codon

src/c/o/cogent-1.5.3/tests/benchmark.py   cogent(Download)
#!/usr/bin/env python
 
import sys #,hotshot
 
from cogent.evolve.substitution_model import Nucleotide, Dinucleotide, Codon