def test_families(self):
""" to check if mutations are correctly retrieved """
self.init_test(self.current_func_name)
abs_fam_db = self.__create_db_instance()
test_file = os.path.join(self.data_dir, self.current_func_name + ".txt")
fam_db = FamilyDB()
fam_db.open_db(test_file)
abs_fam_db.add_connector(fam_db)
families = abs_fam_db.families
# *************** test keys ******************
self.assertEqual(len(families.keys()), 7, "Incorrect number of families keys")
self.assertTrue("8" in families, "Incorrect families key")
self.assertTrue("231" in families, "Incorrect families key")
self.assertTrue("347" not in families, "Incorrect families key")
# *************** test contents ******************
test_family = families["425"]
self.assertEqual(len(test_family.patient_codes), 3, "Incorrect number of members")
self.assertEqual(test_family.type2, "RECTAL", "Incorrect family type2")
self.assertEqual(test_family.type3, "", "Incorrect family type3")
self.assertEqual(test_family.type4, "CAFAM", "Incorrect family type4")
patient_codes = test_family.patient_codes
self.assertEqual(len(patient_codes), 3, "Incorrect number of patient codes being read")
self.assertEqual(patient_codes[0], "Co1458", "Incorrect patient code")
self.assertEqual(patient_codes[1], "Co1595", "Incorrect patient code")
self.assertEqual(patient_codes[2], "Co866", "Incorrect patient code")
def test_group_members_count(self):
"""
to check if number of members in each group are correctly counted
"""
self.init_test(self.current_func_name)
abs_fam_db = self.__create_db_instance()
test_file = os.path.join(self.data_dir, self.current_func_name + ".txt")
fam_db = FamilyDB()
fam_db.open_db(test_file)
abs_fam_db.add_connector(fam_db)
test_group_members_count = abs_fam_db.group_members_count
# *************** test group members count ******************
self.assertEqual(test_group_members_count[TYPE1_ALL], 76, "Invaild number of members in group: " + TYPE1_ALL)
self.assertEqual(
test_group_members_count[TYPE2_RECTAL], 37, "Invaild number of members in group: " + TYPE2_RECTAL
)
self.assertEqual(
test_group_members_count[TYPE2_NON_RECTAL], 39, "Invaild number of members in group: " + TYPE2_NON_RECTAL
)
self.assertEqual(
test_group_members_count[TYPE3_COLON], 21, "Invaild number of members in group: " + TYPE3_COLON
)
self.assertEqual(
test_group_members_count[TYPE3_NON_COLON], 55, "Invaild number of members in group: " + TYPE3_NON_COLON
)
self.assertEqual(
test_group_members_count[TYPE4_CAFAM], 37, "Invaild number of members in group: " + TYPE4_CAFAM
)
self.assertEqual(
test_group_members_count[TYPE4_NON_CAFAM], 39, "Invaild number of members in group: " + TYPE4_NON_CAFAM
)
def __connect_family_db(self, family_db_file):
self.info("creating family db connection to " + family_db_file)
fam_db = FamilyDB()
fam_db.open_db(family_db_file)
self.__abs_fam_db.add_connector(fam_db)
