#!/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 2007-2012, The Cogent Project" __credits__ = ["Peter Maxwell", "Gavin Huttley"] __license__ = "GPL" __version__ = "1.5.3" __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()