def test_parse_msa__single_entry_with_meta():
lines = [">seq1 Meta info", "ACG"]
result_msa = {"seq1": "ACG"}
result_meta = {"seq1": "Meta info"}
with RequiredCall(_VALIDATION_PATH, args=[result_msa]):
msa, meta = parse_msa(lines, read_meta=True)
assert_equal(msa, result_msa)
assert_equal(meta, result_meta)
def test_parse_msa__single_entry_with_meta():
lines = [">seq1 Meta info", "ACG"]
result_msa = {"seq1" : "ACG"}
result_meta = {"seq1" : "Meta info"}
with RequiredCall(_VALIDATION_PATH, args = [result_msa]):
msa, meta = parse_msa(lines, read_meta = True)
assert_equal(msa, result_msa)
assert_equal(meta, result_meta)
def test_parse_msa__two_entries_with_meta():
lines = [">seq1", "ACG", ">seq2 Second meta", "TGA"]
result_msa = {"seq1": "ACG", "seq2": "TGA"}
result_meta = {"seq1": None, "seq2": "Second meta"}
with RequiredCall(_VALIDATION_PATH, args=[result_msa]):
msa, meta = parse_msa(lines, read_meta=True)
assert_equal(msa, result_msa)
assert_equal(meta, result_meta)
def test_parse_msa__two_entries_with_meta():
lines = [">seq1", "ACG", ">seq2 Second meta", "TGA"]
result_msa = {"seq1" : "ACG", "seq2" : "TGA"}
result_meta = {"seq1" : None, "seq2" : "Second meta"}
with RequiredCall(_VALIDATION_PATH, args = [result_msa]):
msa, meta = parse_msa(lines, read_meta = True)
assert_equal(msa, result_msa)
assert_equal(meta, result_meta)
def test_parse_msa__single_entry():
lines = [">seq1", "ACG"]
result = {"seq1": "ACG"}
with RequiredCall(_VALIDATION_PATH, args=[result]):
assert_equal(parse_msa(lines), result)
def test_parse_msa__empty_name():
parse_msa([">", "ACG", ">seq1", "TGAN"])
def test_parse_msa__mismatched_lengths():
parse_msa([">seq1", "ACG", ">seq1", "TGAN"])
def test_parse_msa__duplicate_names():
parse_msa([">seq1", "ACG", ">seq1", "TGA"])
def test_parse_msa__two_entries():
lines = [">seq1", "ACG", ">seq2", "TGA"]
result = {"seq1": "ACG", "seq2": "TGA"}
with RequiredCall(_VALIDATION_PATH, args=[result]):
assert_equal(parse_msa(lines), result)
def test_parse_msa__two_entries():
lines = [">seq1", "ACG", ">seq2", "TGA"]
result = {"seq1" : "ACG", "seq2" : "TGA"}
with RequiredCall(_VALIDATION_PATH, args = [result]):
assert_equal(parse_msa(lines), result)
def test_parse_msa__single_entry():
lines = [">seq1", "ACG"]
result = {"seq1" : "ACG"}
with RequiredCall(_VALIDATION_PATH, args = [result]):
assert_equal(parse_msa(lines), result)
def test_parse_msa__empty_name():
parse_msa([">", "ACG", ">seq1", "TGAN"])
def test_parse_msa__mismatched_lengths():
parse_msa([">seq1", "ACG", ">seq1", "TGAN"])
def test_parse_msa__duplicate_names():
parse_msa([">seq1", "ACG", ">seq1", "TGA"])