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#!/usr/bin/env python
import os
from cogent import LoadSeqs, CodonAlphabet, DNA, LoadTable
from cogent.core import genetic_code
from cogent.evolve import substitution_model, substitution_calculation
from cogent.util.unit_test import TestCase, main
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
base_path = os.getcwd()
data_path = os.path.join(base_path, 'data')
class NucleotideModelTestMethods(TestCase):
def setUp(self):
self.submodel = substitution_model.Nucleotide(
do_scaling=True, model_gaps=False)
def test_isTransition(self):
"""testing isTransition"""
isTransition = self.submodel.getPredefinedPredicate('transition')
assert isTransition('A', 'G')
assert isTransition('C', 'T')
assert not isTransition('A', 'T')
assert not isTransition('C', 'G')
def test_isTransversion(self):
"""testing isTransversion"""
isTransversion = self.submodel.getPredefinedPredicate('transversion')
assert not isTransversion('A', 'G')
assert not isTransversion('C', 'T')
assert isTransversion('A', 'T')
assert isTransversion('C', 'G')
def test_isIndel(self):
"""testing indel comparison nucleotide model"""
model = substitution_model.Nucleotide(
do_scaling=True, model_gaps=True)
isIndel = model.getPredefinedPredicate('indel')
assert isIndel('A', '-')
assert isIndel('-', 'G')
#assert not self.submodel.isIndel('-', '-')
assert not isIndel('a', 't')
def test_PredicateChecks(self):
# overparameterisation
self.assertRaises(ValueError, substitution_model.Nucleotide,
model_gaps=False, predicates=['transition', 'transversion'])
class MultiLetterMotifSubstModelTests(TestCase):
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')
model.asciiArt()
def test_isIndel(self):
"""testing indel comparison for dinucleotide model"""
# these are non-instantaneous
isIndel = self.submodel.getPredefinedPredicate('indel')
assert not isIndel('AA', '--')
assert not isIndel('--', 'CT')
#assert not self.submodel.isIndel('--', '--')
assert not isIndel('AT', 'AA')
assert isIndel('AA', 'A-')
assert isIndel('-A', 'CA')
assert isIndel('TA', '-A')
# isIndel can now assume it won't get any non-instantaneous pairs
# assert self.submodel.isIndel('-a', 'a-') == 0
class TupleModelMotifProbFuncs(TestCase):
dinucs = ('TT', 'CT', 'AT', 'GT',
'TC', 'CC', 'AC', 'GC',
'TA', 'CA', 'AA', 'GA',
'TG', 'CG', 'AG', 'GG')
nuc_probs = [('T', 0.1), ('C', 0.2), ('A', 0.3), ('G', 0.4)]
dinuc_probs=[(m2+m1,p1*p2) for m1,p1 in nuc_probs for m2,p2 in nuc_probs]
mat_indices = dict(
C=set([(0,1),(0,4),(1,5),(2,1),(2,6),(3,1),(3,7),(4,5),(6,5),
(7,5),(8,4),(8,9),(9,5),(10,6),(10,9),(11,7),(11,9),(12,4),
(12,13),(13,5),(14,6),(14,13),(15,7),(15,13)]),
A=set([(0,2),(0,8),(1,2),(1,9),(2,10),(3,2),(3,11),(4,6),(4,8),
(5,6),(5,9),(6,10),(7,6),(7,11),(8,10),(9,10),(11,10),
(12,8),(12,14),(13,9),(13,14),(14,10),(15,11),(15,14)]),
G=set([(0,3),(0,12),(1,3),(1,13),(2,3),(2,14),(3,15),(4,7),(4,12),
(5,7),(5,13),(6,7),(6,14),(7,15),(8,11),(8,12),(9,11),
(9,13),(10,11),(10,14),(11,15),(12,15),(13,15),(14,15)]),
T=set([(1,0),(2,0),(3,0),(4,0),(5,1),(5,4),(6,2),(6,4),(7,3),
(7,4),(8,0),(9,1),(9,8),(10,2),(10,8),(11,3),(11,8),(12,0),
(13,1),(13,12),(14,2),(14,12),(15,3),(15,12)])
)
class ThreeLetterMotifSubstModelTests(TestCase):
def setUp(self):
self.submodel = substitution_model.Nucleotide(motif_length=3,
mprob_model='tuple')
def test_isIndel(self):
"""testing indel comparison for trinucleotide model"""
isIndel = self.submodel.getPredefinedPredicate('indel')
assert isIndel('AAA', 'AA-')
assert isIndel('-CA', 'CCA')
assert isIndel('TAC', 'T-C')
# isIndel can now assume it won't get any non-instantaneous pairs
assert not isIndel('AAA', '---')
assert not isIndel('---', 'CTT')
assert not isIndel('AAA', '--A')
assert not isIndel('C--', 'CTT')
class CodonSubstModelTests(TestCase):
def setUp(self):
self.standardcode = substitution_model.Codon(model_gaps=True, gc=1,
mprob_model='tuple')
self.mitocode = substitution_model.Codon(model_gaps=False, gc=2,
mprob_model='tuple')
def test_isTransition(self):
"""testing codon isTransition"""
isTransition = self.standardcode.getPredefinedPredicate('transition')
# first position
assert isTransition('TGC', 'CGC')
assert isTransition('GGC', 'AGC')
# second position
assert isTransition('CTT', 'CCT')
assert isTransition('CAT', 'CGT')
# thirs position
assert isTransition('CTT', 'CTC')
assert isTransition('CTA', 'CTG')
# mito code
assert isTransition('CTT', 'CTC')
assert isTransition('CTA', 'CTG')
assert not isTransition('GAG', 'GTG')
assert not isTransition('CCC', 'CGC')
def test_isReplacement(self):
"""test isReplacement for the two major genetic codes"""
isReplacement = self.standardcode.getPredefinedPredicate('replacement')
# for the standard code, a replacement
assert isReplacement('CTG', 'ATG')
assert not isReplacement('AGT','TCC')
assert not isReplacement('CTG', '---')
assert not isReplacement('---', 'CTA')
# for the vert mitocho code, instantaneous replacement
isReplacement = self.mitocode.getPredefinedPredicate('replacement')
assert isReplacement('AAA', 'AAC')
def test_isSilent(self):
"""testing isSilent for the two major genetic codes"""
isSilent = self.standardcode.getPredefinedPredicate('silent')
assert isSilent('CTA', 'CTG')
assert not isSilent('AGT','AAG')
assert not isSilent('CTG', '---')
assert not isSilent('---', 'CTG')
# for vert mito code
isSilent = self.mitocode.getPredefinedPredicate('silent')
assert isSilent('TCC', 'TCA')
def test_isIndel(self):
"""test isIndel for codon model"""
isIndel = self.standardcode.getPredefinedPredicate('indel')
assert isIndel('CTA', '---')
assert not isIndel('---', '---')
assert isIndel('---', 'TTC')
def test_str_(self):
"""str() and repr() of a substitution model"""
s = str(self.standardcode)
r = repr(self.standardcode)
class ModelDataInteractionTestMethods(TestCase):
def test_excludeinggaps(self):
"""testing excluding gaps from model"""
model = substitution_model.Nucleotide(model_gaps=False)
assert len(model.getAlphabet()) == 4
def test_includinggaps(self):
"""testing excluding gaps from model"""
model = substitution_model.Nucleotide(model_gaps=True)
assert len(model.getAlphabet()) == 5
def test_getMotifs(self):
"""testing return of motifs"""
model_motifs = substitution_model.Nucleotide().getMotifs()
def test_getParamList(self):
"""testing getting the parameter list"""
model = substitution_model.Nucleotide()
self.assertEqual(model.getParamList(), [])
model = substitution_model.Nucleotide(predicates=['beta:transition'])
self.assertEqual(model.getParamList(), ['beta'])
# need to ensure entering motif probs that sum to 1, that motif sets are the same
if __name__ == '__main__':
main()
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