def test_find_new_variants_one_diff_cant_assign(self):
res = assemble.find_new_variants(
self.ref, {
'A': [self.aln2, self.aln3],
'B': [self.aln2, self.aln3],
'unassigned': [self.aln1]
}, self.args)
exp = {}
self.assertEqual(res, exp)
def test_find_new_variants_one_diff_two_contributors(self):
res = assemble.find_new_variants(
self.ref, {
'A': [self.aln2, self.aln2],
'B': [self.aln3, self.aln3],
'unassigned': [self.aln1]
}, self.args)
exp = {(15, 'A'): 'A', (15, 'T'): 'B'}
self.assertEqual(res, exp)
def test_find_new_variants_none_to_find(self):
res = assemble.find_new_variants(
self.ref, {
'A': [self.aln1, self.aln2],
'B': [self.aln1, self.aln1],
'unassigned': [self.aln3]
}, self.args)
exp = {}
self.assertEqual(res, exp)
def test_find_new_variants_two_diff_missing_cov_three_contributors(self):
self.aln1.query_sequence = "AAGAA"
res = assemble.find_new_variants(
self.ref, {
'A': [self.aln2, self.aln2],
'B': [self.aln3, self.aln3],
'C': [self.aln1, self.aln2, self.aln2],
'unassigned': [self.aln1]
}, self.args)
# A13G variant is only covered in hap 'C'. Cannot call new variant.
exp = {(15, 'T'): 'B'}
self.assertEqual(res, exp)
def test_find_new_variants_one_diff_three_contributors(self):
res = assemble.find_new_variants(
self.ref, {
'A': [self.aln2, self.aln2],
'B': [self.aln3, self.aln3],
'C': [self.aln2, self.aln2],
'unassigned': [self.aln1]
}, self.args)
# base 'T' can be assigned to hap 'B', but 'A' cannot be assigned
# because 'A' and 'C' both have 'A'.
exp = {(15, 'T'): 'B'}
self.assertEqual(res, exp)
def test_find_new_variants_empty_input(self):
res = assemble.find_new_variants(self.ref, {}, self.args)
exp = {}
self.assertEqual(res, exp)