def setUp(self):
self.reference_paths = [
'no_intersections/no_intersections_ref',
'three_same_children/three_same_children_ref',
'two_same_one_unique/two_same_one_unique_ref',
'aa_ab_ac_ab_ac/aa_ab_ac_ab_ac_ref',
'aa_ab_bb_ab_ab/aa_ab_bb_ab_ab_ref',
'aa_ab_bc_ab_ac/aa_ab_bc_ab_ac_ref',
'aa_ab_bc_ac_ab/aa_ab_bc_ac_ab_ref',
'ab_ac_bc_ab_acbc/ab_ac_bc_ab_acbc_ref',
'ab_ac_bd_ac_bd/ab_ac_bd_ac_bd_ref'
]
self.test_paths = [
'no_intersections/no_intersections_test',
'three_same_children/three_same_children_test',
'two_same_one_unique/two_same_one_unique_test',
'aa_ab_ac_ab_ac/aa_ab_ac_ab_ac_test',
'aa_ab_bb_ab_ab/aa_ab_bb_ab_ab_test',
'aa_ab_bc_ab_ac/aa_ab_bc_ab_ac_test',
'aa_ab_bc_ac_ab/aa_ab_bc_ac_ab_test',
'ab_ac_bc_ab_acbc/ab_ac_bc_ab_acbc_test',
'ab_ac_bd_ac_bd/ab_ac_bd_ac_bd_test'
]
short_path = 'cognation/scripts/tests/test_cases/three_known_supposed_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(short_path, test_path, 6)
def setUp(self):
self.reference_paths = [
'no_intersections/no_intersections_ref',
'same_genotypes/same_genotypes_ref', 'aa_ab_ab_an/aa_ab_ab_an_ref',
'aa_ab_an_ab/aa_ab_an_ab_ref', 'aa_bb_ab_ab/aa_bb_ab_ab_ref',
'aa_bc_ab_ac/aa_bc_ab_ac_ref', 'ab_ac_ab_acbc/ab_ac_ab_acbc_ref',
'ab_ac_an_bc/ab_ac_an_bc_ref', 'ab_ac_bc_an/ab_ac_bc_an_ref',
'ab_cd_bd_ac/ab_cd_bd_ac_ref'
]
self.test_paths = [
'no_intersections/no_intersections_test',
'same_genotypes/same_genotypes_test',
'aa_ab_ab_an/aa_ab_ab_an_test', 'aa_ab_an_ab/aa_ab_an_ab_test',
'aa_bb_ab_ab/aa_bb_ab_ab_test', 'aa_bc_ab_ac/aa_bc_ab_ac_test',
'ab_ac_ab_acbc/ab_ac_ab_acbc_test', 'ab_ac_an_bc/ab_ac_an_bc_test',
'ab_ac_bc_an/ab_ac_bc_an_test', 'ab_cd_bd_ac/ab_cd_bd_ac_test'
]
short_path = 'cognation/scripts/tests/test_cases/two_known_supposed_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(
short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(
short_path, test_path, 5)
def setUp(self):
self.reference_paths = [
'no_intersections/no_intersections_ref',
'1_calls_ParentFormula/1_calls_ParentFormula_ref',
'2_aa_an_an/2_aa_an_an_ref',
'3_aa_bb_ab/3_aa_bb_ab_ref',
'4_aa_bc_abac/4_aa_bc_abac_ref',
'5_ab_ac_anbc/5_ab_ac_anbc_ref',
'6_ab_cc_acbc/6_ab_cc_acbc_ref',
'7_ab_cd_acadbcbd/7_ab_cd_acadbcbd_ref'
]
self.test_paths = [
'no_intersections/no_intersections_test',
'1_calls_ParentFormula/1_calls_ParentFormula_test',
'2_aa_an_an/2_aa_an_an_test',
'3_aa_bb_ab/3_aa_bb_ab_test',
'4_aa_bc_abac/4_aa_bc_abac_test',
'5_ab_ac_anbc/5_ab_ac_anbc_test',
'6_ab_cc_acbc/6_ab_cc_acbc_test',
'7_ab_cd_acadbcbd/7_ab_cd_acadbcbd_test'
]
short_path = 'cognation/scripts/tests/test_cases/twochildren_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(short_path, test_path, 2)
def setUp(self):
self.reference_paths = [
'no_intersections/no_intersections_ref',
'call_CoupleFormula/call_CoupleFormula_ref',
'call_TwoCouple_Formula/call_TwoCouple_Formula_ref',
'aa_ab_ac_ab_ac/aa_ab_ac_ab_ac_ref',
'aa_ab_bb_ab_ab/aa_ab_bb_ab_ab_ref',
'ab_ac_bc_ab_ac/ab_ac_bc_ab_ac_ref',
'ab_ac_bc_ab_bc/ab_ac_bc_ab_bc_ref',
'ab_ac_bc_ac_bc/ab_ac_bc_ac_bc_ref',
'ab_ac_bd_ac_bd/ab_ac_bd_ac_bd_ref'
]
self.test_paths = [
'no_intersections/no_intersections_test',
'call_CoupleFormula/call_CoupleFormula_test',
'call_TwoCouple_Formula/call_TwoCouple_Formula_test',
'aa_ab_ac_ab_ac/aa_ab_ac_ab_ac_test',
'aa_ab_bb_ab_ab/aa_ab_bb_ab_ab_test',
'ab_ac_bc_ab_ac/ab_ac_bc_ab_ac_test',
'ab_ac_bc_ab_bc/ab_ac_bc_ab_bc_test',
'ab_ac_bc_ac_bc/ab_ac_bc_ac_bc_test',
'ab_ac_bd_ac_bd/ab_ac_bd_ac_bd_test'
]
short_path = 'cognation/scripts/tests/test_cases/three_couple_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(short_path, test_path, 10)
def prep(self):
get_ref = GetData()
for i in range(len(doc_refnames_list)):
doc_ref_path = doc_refnames_list[i]
overall_ref_dict[doc_ref_path] = get_ref.get_reference_data(
short_path, doc_ref_path)
doc_test_path = doc_testnames_list[i]
overall_test_dict[doc_test_path] = get_ref.get_test_data(
short_path, doc_test_path, STEPBROTHER_TYPE)
def setUp(self):
self.reference_paths, self.test_paths = ['sister1/sister1_ref'], ['sister1/sister1_test']
short_path = 'cognation/scripts/tests/test_cases/brother_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(short_path, test_path, 12)
pass
def setUp(self):
self.reference_paths = ['case1/case1_ref', 'case2/case2_ref']
self.test_paths = ['case1/case1_test', 'case2/case2_test']
short_path = 'cognation/scripts/tests/test_cases/yes_parent_grand_child_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(
short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(
short_path, test_path, 19)
def setUp(self):
self.reference_paths = [
'sibling1/sibling1_ref', 'sibling2/sibling2_ref'
]
self.test_paths = ['sibling1/sibling1_test', 'sibling2/sibling2_test']
short_path = 'cognation/scripts/tests/test_cases/sibling_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(
short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(
short_path, test_path, 3)
def setUp(self):
self.reference_paths = [
'no_intersections/no_intersections_ref',
'three_same/three_same_ref',
'two_same_one_unique/two_same_one_unique_ref',
'aa_ab_ac_an/aa_ab_ac_an_ref',
'aa_ab_bb_ab/aa_ab_bb_ab_ref',
'aa_ab_bc_abac/aa_ab_bc_abac_ref',
'aa_ab_cc_ac/aa_ab_cc_ac_ref',
'aa_bc_bn_ab/aa_bc_bn_ab_ref',
'ab_ac_ad_an/ab_ac_ad_an_ref',
'ab_ac_bc_abacbc/ab_ac_bc_abacbc_ref',
'ab_ac_bd_adbc/ab_ac_bd_adbc_ref',
'ab_ac_сd_acadbc/ab_ac_сd_acadbc_ref',
'ab_ac_de_adae/ab_ac_de_adae_ref',
'ab_cd_cn_acbc/ab_cd_cn_acbc_ref',
]
self.test_paths = [
'no_intersections/no_intersections_test',
'three_same/three_same_test',
'two_same_one_unique/two_same_one_unique_test',
'aa_ab_ac_an/aa_ab_ac_an_test',
'aa_ab_bb_ab/aa_ab_bb_ab_test',
'aa_ab_bc_abac/aa_ab_bc_abac_test',
'aa_ab_cc_ac/aa_ab_cc_ac_test',
'aa_bc_bn_ab/aa_bc_bn_ab_test',
'ab_ac_ad_an/ab_ac_ad_an_test',
'ab_ac_bc_abacbc/ab_ac_bc_abacbc_test',
'ab_ac_bd_adbc/ab_ac_bd_adbc_test',
'ab_ac_сd_acadbc/ab_ac_сd_acadbc_test',
'ab_ac_de_adae/ab_ac_de_adae_test',
'ab_cd_cn_acbc/ab_cd_cn_acbc_test',
]
short_path = 'cognation/scripts/tests/test_cases/threechildren_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(
short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(
short_path, test_path, 4)
def setUp(self):
self.reference_paths = ['parent1/reference_data_parent1',
'parent2/reference_data_parent2',
'parent3/reference_data_parent3_veri']
self.test_paths = [
'parent1/test_data_parent1',
'parent2/test_data_parent2',
'parent3/test_data_parent3_veri'
]
short_path = 'cognation/scripts/tests/test_cases/parent_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(short_path, test_path, 1)
pass
def setUp(self):
self.reference_paths = [
'no_intersections/no_intersections_ref',
'aa_an_an/aa_an_an_ref',
'ab_an_bn/ab_an_bn_ref'
]
self.test_paths = [
'no_intersections/no_intersections_test',
'aa_an_an/aa_an_an_test',
'ab_an_bn/ab_an_bn_test'
]
short_path = 'cognation/scripts/tests/test_cases/couple_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(short_path, test_path, 7)
pass
def setUp(self):
self.reference_paths = [
'brother_1/brother_1_ref',
'brother_2/brother_2_ref',
'zero_cases/zero_cases_ref'
]
self.test_paths = [
'brother_1/brother_1_test',
'brother_2/brother_2_test',
'zero_cases/zero_cases_test'
]
short_path = 'cognation/scripts/tests/test_cases/two_brothers_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(short_path, test_path, 13)
def setUp(self):
self.reference_paths = [
#'hetero_1/both_hetero_ref1',
#'hetero_2/both_hetero_ref2',
'h**o/homo_ref'
]
self.test_paths = [
#'hetero_1/both_hetero_test1',
#'hetero_2/both_hetero_test2',
'h**o/homo_test'
]
short_path = 'cognation/scripts/tests/test_cases/both_grandparents_cases/'
get_ref = GetData()
self.overall_ref_dict, self.overall_test_dict = {}, {}
for i in range(len(self.reference_paths)):
ref_path, test_path = self.reference_paths[i], self.test_paths[i]
self.overall_ref_dict[ref_path] = get_ref.get_reference_data(
short_path, ref_path)
self.overall_test_dict[test_path] = get_ref.get_test_data(
short_path, test_path, 18)
pass