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#!/usr/bin/env python
import unittest
from cogent3.core.moltype import CodonAlphabet
from cogent3.evolve.predicate import MotifChange, parse
class FakeModel(object):
def __init__(self, alphabet):
self.alphabet = alphabet
self.moltype = alphabet.moltype
def get_alphabet(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 test_parse(self):
"""correctly construction"""
ag = MotifChange("A", "G")
got = parse(str(ag))
self.assertEqual(str(got), "A/G")
ts = MotifChange("A", "G") | MotifChange("C", "T")
got = parse(str(ts))
self.assertEqual(str(got), "(A/G | C/T)")
a_g = MotifChange("A", "G", forward_only=True)
t_c = MotifChange("T", "C", forward_only=True)
sym = a_g | t_c
got = parse(str(sym))
self.assertEqual(str(got), "(A>G | T>C)")
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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