def test_stringcase(self): orig_allele_origins = ['Germline'] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([['germline']], converted_allele_origins) orig_allele_origins = ['SOMATIC'] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([['somatic']], converted_allele_origins)
def test_nonsense(self): orig_allele_origins_list = [["fgdsgfgs"], ["notarealorigin"], ["134312432:dasdfd"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins(orig_allele_origins) self.assertListEqual([], converted_allele_origins) orig_allele_origins = ["fgdsgfgs", "germline"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins(orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins)
def test_mixed(self): orig_allele_origins = ['germline', 'somatic'] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([['somatic'], ['germline']], converted_allele_origins) orig_allele_origins = ['somatic', 'inherited', 'not applicable'] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([['somatic'], ['inherited', 'not applicable']], converted_allele_origins)
def test_nonsense(self): orig_allele_origins_list = [["fgdsgfgs"], ["notarealorigin"], ["134312432:dasdfd"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([], converted_allele_origins) orig_allele_origins = ["fgdsgfgs", "germline"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins)
def test_stringcase(self): orig_allele_origins_list = [["Germline"], ["InHerIted"], ["UNKNOWN"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins) orig_allele_origins_list = [["Somatic"], ["SOMATIC"], ["sOMatIc"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["somatic"], converted_allele_origins)
def test_duplicate(self): orig_allele_origins = ["germline", "germline"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins) orig_allele_origins = ["inherited", "inherited", "germline"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins) orig_allele_origins = ["somatic", "somatic", "somatic"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["somatic"], converted_allele_origins)
def test_duplicate(self): orig_allele_origins = ["germline", "germline"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins) orig_allele_origins = ["inherited", "inherited", "germline"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins) orig_allele_origins = ["somatic", "somatic", "somatic"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["somatic"], converted_allele_origins)
def test_stringcase(self): orig_allele_origins_list = [["Germline"], ["InHerIted"], ["UNKNOWN"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins(orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins) orig_allele_origins_list = [["Somatic"], ["SOMATIC"], ["sOMatIc"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["somatic"], converted_allele_origins)
def test_just_other_germline(self): orig_allele_origins_list = [["unknown"], ["inherited"], ["maternal"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins(orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins)
def test_mixed(self): orig_allele_origins_list = [["germline", "somatic"], ["somatic", "inherited", "not applicable"], ["somatic", "unknown"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["somatic", "germline"], converted_allele_origins)
def test_mixed(self): orig_allele_origins_list = [["germline", "somatic"], ["somatic", "inherited", "not applicable"], ["somatic", "unknown"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["somatic", "germline"], converted_allele_origins)
def test_missing(self): orig_allele_origins = [] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([[]], converted_allele_origins)
def test_just_germline(self): orig_allele_origins = ['germline'] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([['germline']], converted_allele_origins)
def test_just_somatic(self): orig_allele_origins = ["somatic"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins(orig_allele_origins) self.assertListEqual(["somatic"], converted_allele_origins)
def test_just_other_germline(self): orig_allele_origins_list = [["unknown"], ["inherited"], ["maternal"]] for orig_allele_origins in orig_allele_origins_list: converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["germline"], converted_allele_origins)
def test_just_tested_inconclusive(self): orig_allele_origins = ["tested-inconclusive"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual([], converted_allele_origins)
def test_just_somatic(self): orig_allele_origins = ["somatic"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins( orig_allele_origins) self.assertListEqual(["somatic"], converted_allele_origins)
def test_just_tested_inconclusive(self): orig_allele_origins = ["tested-inconclusive"] converted_allele_origins = clinvar_to_evidence_strings.convert_allele_origins(orig_allele_origins) self.assertListEqual([], converted_allele_origins)