def test_parse_parents_no_mother(self):
vcf_test = vcf(self.proband_index_QTB[0], self.number_affected_QTB[0],
self.mom_absent)
self.assertEqual(
vcf_test.parseAbsentParents(), [False, True],
"Mother was not recognized as absent and/or father was not recognized as present."
)
def person_generator(self, person):
new_person = vcf(
self.June_Cohort[person]["index"],
self.June_Cohort[person]["num_affected"],
self.June_Cohort[person]["absent"], self.snv_file_June,
self.indel_file_June, self.pedigree[0],
"/home/alex/Documents/Frankie_Analysis/SOLVE_BRAIN_TEST/")
new_person.computeParents()
return new_person
def test_compute_XL_false_one_parent_inherited_from_dad(self):
vcf_test = vcf(self.June_Cohort["MP14-004"]["index"],
self.June_Cohort["MP14-004"]["num_affected"],
self.mom_absent)
vcf_test.computeParents()
self.assertFalse(
vcf_test.computeXL(self.vcf_line_with_XL_2),
"Compute XL did not recognize that proband has variant from father"
)
def test_compute_parents_june_cohort(self):
for proband in self.June_Cohort:
vcf_test = vcf(self.June_Cohort[proband]["index"],
self.June_Cohort[proband]["num_affected"],
self.June_Cohort[proband]["absent"])
self.assertEqual(
vcf_test.computeParents(),
self.June_Cohort[proband]["parents"],
"Parent indecies not computed correctly for June cohort")
def test_compute_parents_no_father(self):
for index in range(len(self.proband_index_QTB)):
vcf_test = vcf(self.proband_index_QTB[index],
self.number_affected_QTB[index], self.dad_absent)
vcf_test.parseAbsentParents()
self.assertEqual(vcf_test.computeParents(), [
0,
self.proband_index_QTB[index] + self.number_affected_QTB[index]
])
def test_map_return_array_length(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"],
self.entire_cohort,
self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
self.assertEqual(
len(
vcf_test.mapSearch("0/0",
self.map_return_all_ONE_ONE.split('\t'))),
38)
def test_map_return_all_false(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"],
self.entire_cohort,
self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
self.assertFalse(
all(
vcf_test.mapSearch("0/0",
self.map_return_all_ONE_ONE.split('\t'))),
"Map Return thought a 0/0 existed when it did not")
def test_map_return_all_true(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"],
self.entire_cohort,
self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
self.assertTrue(
all(
vcf_test.mapSearch(
"1/1", self.map_return_all_ONE_ONE.split('\t'))[24:]),
"Map Return thought did not find all to be true searching for 1/1")
def test_vcf_line_computation_homo(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"],
self.entire_cohort,
self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
returned_array = vcf_test.computeVCFLine(
self.vcf_line_all_three_cases)['h**o']
self.assertTrue(
all([returned_array[24], returned_array[30]]),
"Compute VCF lines did not find the homozygous(1/1) cases correctly"
)
def test_map_return_last_true_only(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"],
self.entire_cohort,
self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
returned_array = vcf_test.mapSearch(
"0/1", self.map_return_last_true.split('\t'))
self.assertFalse(all(returned_array[24:len(returned_array) - 1]),
"Map Return find a 0/1 in a sea of all 0/0")
self.assertTrue(returned_array[len(returned_array) - 1:][0],
"Map Return did not find the last index to be 0/1")
def test_vcf_line_computation_hetero(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"],
self.entire_cohort,
self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
returned_array = vcf_test.computeVCFLine(
self.vcf_line_all_three_cases)['hetero']
self.assertTrue(
all([
returned_array[26], returned_array[27], returned_array[28],
returned_array[34], returned_array[35], returned_array[36],
returned_array[37]
]),
"Compute VCF lines did not find the absent(0/0) cases correctly")
def test_map_return_last_true_only(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"], self.entire_cohort, self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
returned_array = vcf_test.mapSearch("0/1", self.map_return_last_true.split('\t'))
self.assertFalse(all(returned_array[24:len(returned_array) - 1]), "Map Return find a 0/1 in a sea of all 0/0")
self.assertTrue(returned_array[len(returned_array) - 1:][0], "Map Return did not find the last index to be 0/1")
def test_parse_parents_both_absent(self): vcf_test = vcf(self.proband_index_QTB[0], self.number_affected_QTB[0], self.both_absent) self.assertEqual(vcf_test.parseAbsentParents(), [True, True], "Parents were not recognized as both being absent")
def test_vcf_line_computation_absent(self): vcf_test = vcf(self.June_Cohort["DB14-001"]["index"], self.entire_cohort, self.June_Cohort["DB14-001"]["absent"]) vcf_test.computeParents() returned_array = vcf_test.computeVCFLine(self.vcf_line_all_three_cases)['absent'] self.assertTrue(all([returned_array[25], returned_array[29], returned_array[31], returned_array[32], returned_array[33]]), "Compute VCF lines did not find the heterozygous(0/1) cases correctly")
def test_vcf_line_computation_hetero(self): vcf_test = vcf(self.June_Cohort["DB14-001"]["index"], self.entire_cohort, self.June_Cohort["DB14-001"]["absent"]) vcf_test.computeParents() returned_array = vcf_test.computeVCFLine(self.vcf_line_all_three_cases)['hetero'] self.assertTrue(all([returned_array[26], returned_array[27], returned_array[28], returned_array[34], returned_array[35], returned_array[36], returned_array[37]]), "Compute VCF lines did not find the absent(0/0) cases correctly")
def test_compute_XL_false_one_parent_inherited_from_dad(self): vcf_test = vcf(self.June_Cohort["MP14-004"]["index"], self.June_Cohort["MP14-004"]["num_affected"], self.mom_absent) vcf_test.computeParents() self.assertFalse(vcf_test.computeXL(self.vcf_line_with_XL_2), "Compute XL did not recognize that proband has variant from father")
def person_generator(self, person): new_person = vcf(self.June_Cohort[person]["index"], self.June_Cohort[person]["num_affected"], self.June_Cohort[person]["absent"], self.snv_file_June, self.indel_file_June, self.pedigree[0], "/home/alex/Documents/Frankie_Analysis/SOLVE_BRAIN_TEST/") new_person.computeParents() return new_person
def test_map_return_all_true(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"], self.entire_cohort, self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
self.assertTrue(all(vcf_test.mapSearch("1/1", self.map_return_all_ONE_ONE.split('\t'))[24:]), "Map Return thought did not find all to be true searching for 1/1")
def test_parse_parents_no_absent(self): vcf_test = vcf(self.proband_index_QTB[0], self.number_affected_QTB[0], self.no_absent) self.assertEqual(vcf_test.parseAbsentParents(), [False, False], "Parents were not recognized as absent.")
def test_parse_parents_no_father(self): vcf_test = vcf(self.proband_index_QTB[0], self.number_affected_QTB[0], self.dad_absent) self.assertEqual(vcf_test.parseAbsentParents(), [True, False], "Father was not recognized as absent and/or mother was not recognized as present.")
def test_parse_parents_no_absent(self):
vcf_test = vcf(self.proband_index_QTB[0], self.number_affected_QTB[0],
self.no_absent)
self.assertEqual(vcf_test.parseAbsentParents(), [False, False],
"Parents were not recognized as absent.")
def test_map_return_array_length(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"], self.entire_cohort, self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
self.assertEqual(len(vcf_test.mapSearch("0/0", self.map_return_all_ONE_ONE.split('\t'))), 38)
def test_compute_parents_no_absent(self): for index in range(len(self.proband_index_QTB)): vcf_test = vcf(self.proband_index_QTB[index], self.number_affected_QTB[index], self.no_absent) vcf_test.parseAbsentParents() self.assertEqual(vcf_test.computeParents(), [self.proband_index_QTB[index] + self.number_affected_QTB[index], self.proband_index_QTB[index] + self.number_affected_QTB[index] + 1])
def test_map_return_all_false(self):
vcf_test = vcf(self.June_Cohort["DB14-001"]["index"], self.entire_cohort, self.June_Cohort["DB14-001"]["absent"])
vcf_test.computeParents()
self.assertFalse(all(vcf_test.mapSearch("0/0", self.map_return_all_ONE_ONE.split('\t'))), "Map Return thought a 0/0 existed when it did not")
def test_parse_parents_both_absent(self):
vcf_test = vcf(self.proband_index_QTB[0], self.number_affected_QTB[0],
self.both_absent)
self.assertEqual(vcf_test.parseAbsentParents(), [True, True],
"Parents were not recognized as both being absent")
def test_compute_parents_june_cohort(self): for proband in self.June_Cohort: vcf_test = vcf(self.June_Cohort[proband]["index"], self.June_Cohort[proband]["num_affected"], self.June_Cohort[proband]["absent"]) self.assertEqual(vcf_test.computeParents(), self.June_Cohort[proband]["parents"], "Parent indecies not computed correctly for June cohort")
