class Test_Parsing_Detail_Line(unittest.TestCase):
def setUp(self):
self.parser = DetailParser()
def test_correctly_parses_genesis_detail_line(self):
result = self.parser.process_line(genesisDetailLine)
expected_result = ('1', None, None, None, None,
None, 'wzcagcccccccccccccccccccccccccccccccccccczvfcaxgab')
self.assertTupleEqual(result, expected_result)
def test_correctly_parses_detail_line_with_no_mutations(self):
result = self.parser.process_line(detailLineWithNoMutations)
expected_result = ('72','3', '18', None, None,
'Swp14-26', 'wzcagcccccccccccccccccccbccccccmccccccccczvfcaxgab')
self.assertTupleEqual(result, expected_result)
def test_correctly_parses_detail_line_with_one_mutation(self):
result = self.parser.process_line(detailLineWithOneMutation)
expected_result = ('1055','781', '781', 'Mc13y', None,
'Swp25-38', 'wzcagccccccccyccccccccwcccccccccccrcccccczvfcaxgab')
self.assertTupleEqual(result, expected_result)
def test_correctly_parses_detail_line_with_two_mutations(self):
result = self.parser.process_line(detailLineWithTwoMutations)
expected_result = ('79496','30490', '57433', 'Mc15y', 'Mc40z',
'Swp9-16', 'wzcagccccccccccycpcccehccccckccccckpcccczzvfcaxgab')
self.assertTupleEqual(result, expected_result)
def test_returns_nothing_for_incorrect_detail(self):
detail_line = "123123 2312321 123123"
result = self.parser.process_line(detail_line)
self.assertIsNone(result)
def build_genealogy(self, detailDump):
'''Build and return a Genealogy object by adding Genotypes parsed from
a detail dump'''
parser = DetailParser()
genealogy = Genealogy()
for line in detailDump:
details = parser.process_line(line)
if details:
genealogy.add_genotype(Genotype(*details))
GenotypeRelationshipTool().\
create_relationships_between_genotypes_in_genealogy(genealogy)
return genealogy
def setUp(self):
self.parser = DetailParser()
