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#!/usr/bin/env python
import unittest
from cogent.evolve.predicate import MotifChange
from cogent.core.moltype import CodonAlphabet
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",
"Matthew Wakefield", "Brett Easton"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
class FakeModel(object):
def __init__(self, alphabet):
self.alphabet = alphabet
self.MolType = alphabet.MolType
def getAlphabet(self):
return self.alphabet
class TestPredicates(unittest.TestCase):
def setUp(self):
self.alphabet = CodonAlphabet()
self.model = FakeModel(self.alphabet)
def _makeMotifChange(self, *args, **kw):
pred = MotifChange(*args, **kw)
return pred.interpret(self.model)
def assertMatch(self, pred, seq1, seq2):
assert pred(seq1, seq2), (pred.__doc__, (seq1, seq2))
def assertNoMatch(self, pred, seq1, seq2):
assert not pred(seq1, seq2), ('not ' + pred.__doc__, (seq1, seq2))
def test_indels(self):
indel = self._makeMotifChange('---', 'NNN')
self.assertMatch(indel, '---', 'AAA')
def test_impossible_change(self):
self.assertRaises(Exception,
self._makeMotifChange, '----', 'NNNN')
def test_isfromcpg(self):
isFromCpG = self._makeMotifChange('CG', forward_only = True)
self.assertMatch(isFromCpG, 'CG', 'CA')
self.assertMatch(isFromCpG, 'CG', 'TG')
self.assertMatch(isFromCpG, 'ACG', 'ATG')
self.assertMatch(isFromCpG, 'CGT', 'CTT')
self.assertNoMatch(isFromCpG, 'CTT', 'CGT')
self.assertNoMatch(isFromCpG, 'C', 'G')
def test_isfromtocpg(self):
isFromToCpG = self._makeMotifChange('CG')
self.assertMatch(isFromToCpG, 'CG', 'CA')
self.assertMatch(isFromToCpG, 'CG', 'TG')
self.assertMatch(isFromToCpG, 'ACG', 'ATG')
self.assertMatch(isFromToCpG, 'CGT', 'CTT')
self.assertMatch(isFromToCpG, 'CTT', 'CGT')
def test_isFromToCpA_C_only(self):
isFromToCpA_C_only = self._makeMotifChange('CA', diff_at = 0)
self.assertMatch(isFromToCpA_C_only, 'CA', 'TA')
self.assertMatch(isFromToCpA_C_only, 'TCA', 'TTA')
self.assertMatch(isFromToCpA_C_only, 'TAA', 'CAA')
self.assertNoMatch(isFromToCpA_C_only, 'TCA', 'TCT')
def test_isFromCpA_C_only(self):
isFromCpA_C_only = self._makeMotifChange('CA', forward_only = True, diff_at = 0)
self.assertMatch(isFromCpA_C_only, 'CA', 'TA')
self.assertMatch(isFromCpA_C_only, 'TCA', 'TTA')
self.assertNoMatch(isFromCpA_C_only, 'TAA', 'CAA')
def test_isCpT_T_only(self):
isCpT_T_only = self._makeMotifChange('CT', diff_at = 1)
self.assertMatch(isCpT_T_only, 'CT', 'CA')
self.assertMatch(isCpT_T_only, 'TCA', 'TCT')
self.assertNoMatch(isCpT_T_only, 'TTA', 'TCA')
self.assertNoMatch(isCpT_T_only, 'TA', 'CT')
def test_isCCC(self):
isCCC = self._makeMotifChange('CCC')
self.assertNoMatch(isCCC, 'CC', 'CT')
def test_isC(self):
isC = self._makeMotifChange('C')
self.assertMatch(isC, 'C', 'T')
self.assertNoMatch(isC, 'CA', 'CT')
self.assertMatch(isC, 'CA', 'CC')
self.assertMatch(isC, 'CAT', 'GAT')
self.assertMatch(isC, 'CAT', 'CCT')
self.assertMatch(isC, 'CAT', 'CAC')
self.assertNoMatch(isC, 'CAT', 'CAA')
self.assertNoMatch(isC, 'C', 'C')
def test_isCtoT(self):
isCtoT = self._makeMotifChange('C', 'T')
self.assertMatch(isCtoT, 'C', 'T')
self.assertMatch(isCtoT, 'T', 'C')
self.assertNoMatch(isCtoT, 'T', 'A')
isCtoT = self._makeMotifChange('C', 'T', forward_only = True)
self.assertMatch(isCtoT, 'C', 'T')
self.assertNoMatch(isCtoT, 'T', 'C')
def test_isCGtoCA(self):
isCG_CA = self._makeMotifChange('CG', 'CA')
self.assertMatch(isCG_CA, 'CG', 'CA')
self.assertMatch(isCG_CA, 'CA', 'CG')
self.assertMatch(isCG_CA, 'CAT', 'CGT')
self.assertMatch(isCG_CA, 'CGT', 'CAT')
self.assertMatch(isCG_CA, 'TCA', 'TCG')
self.assertNoMatch(isCG_CA, 'TCT', 'TCG')
self.assertMatch(isCG_CA, 'CGTT', 'CATT')
self.assertMatch(isCG_CA, 'TCGT', 'TCAT')
self.assertMatch(isCG_CA, 'TTCG', 'TTCA')
self.assertMatch(isCG_CA, 'CATT', 'CGTT')
self.assertMatch(isCG_CA, 'TCAT', 'TCGT')
self.assertMatch(isCG_CA, 'TTCA', 'TTCG')
isCG_CA = self._makeMotifChange('CG', 'CA', forward_only = True)
self.assertMatch(isCG_CA, 'CGTT', 'CATT')
self.assertMatch(isCG_CA, 'TCGT', 'TCAT')
self.assertMatch(isCG_CA, 'TTCG', 'TTCA')
self.assertNoMatch(isCG_CA, 'CATT', 'CGTT')
self.assertNoMatch(isCG_CA, 'TCAT', 'TCGT')
self.assertNoMatch(isCG_CA, 'TTCA', 'TTCG')
isCG = self._makeMotifChange('CG', diff_at = 1)
self.assertMatch(isCG, 'CGTT', 'CATT')
self.assertMatch(isCG, 'TCGT', 'TCAT')
self.assertMatch(isCG, 'TTCG', 'TTCA')
self.assertNoMatch(isCG, 'CGTT', 'TGTT')
self.assertNoMatch(isCG, 'TCGT', 'TAGT')
self.assertNoMatch(isCG, 'TTCG', '--GG')
def test_wildcards(self):
isCG_CN = self._makeMotifChange('CG', 'CN')
self.assertMatch(isCG_CN, 'CG', 'CA')
self.assertNoMatch(isCG_CN, 'CG', 'CG')
self.assertNoMatch(isCG_CN, 'CG', 'C-')
if __name__ == '__main__':
unittest.main()
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