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from cogent.util.unit_test import TestCase, main
from cogent.evolve.models import JC69, F81, HKY85, GTR, \
MG94HKY, MG94GTR, GY94, H04G, H04GK, H04GGK, \
DSO78, AH96, AH96_mtmammals, JTT92, WG01, CNFGTR, CNFHKY, \
WG01_matrix, WG01_freqs
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
class CannedModelsTest(TestCase):
"""Check each canned model can actually be instantiated."""
def _instantiate_models(self, models, **kwargs):
for model in models:
model(**kwargs)
def test_nuc_models(self):
"""excercising nucleotide model construction"""
self._instantiate_models([JC69, F81, HKY85, GTR])
def test_codon_models(self):
"""excercising codon model construction"""
self._instantiate_models([CNFGTR, CNFHKY, MG94HKY, MG94GTR, GY94,
H04G, H04GK, H04GGK])
def test_aa_models(self):
"""excercising aa model construction"""
self._instantiate_models([DSO78, AH96, AH96_mtmammals, JTT92, WG01])
def test_bin_options(*self):
kwargs = dict(with_rate=True, distribution='gamma')
model = WG01(**kwargs)
model = GTR(**kwargs)
def test_empirical_values_roundtrip(*self):
model = WG01()
assert model.getMotifProbs() == WG01_freqs
assert (model.calcExchangeabilityMatrix('dummy_mprobs') ==
WG01_matrix).all()
if __name__ == '__main__':
main()
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