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)
