def test_parse_with_parameters(tmp_path):
parser = AdapterParser(max_errors=0.2,
min_overlap=4,
read_wildcards=False,
adapter_wildcards=False,
indels=False)
a = parser._parse('ACGTACGT; e=0.15', 'front')
assert isinstance(a, FrontAdapter)
assert a.max_error_rate == 0.15
assert a.min_overlap == 4
a = parser._parse('ACGTAAAA; o=5; e=0.11', 'back')
assert isinstance(a, BackAdapter)
assert a.max_error_rate == 0.11
assert a.min_overlap == 5
for spec in ('thename=ACG;e=0.15 ... TGT;e=0.17',
'thename=ACG;e=0.15...TGT;e=0.17'):
a = parser._parse(spec, 'back')
assert isinstance(a, LinkedAdapter)
assert a.front_adapter.max_error_rate == 0.15
assert a.back_adapter.max_error_rate == 0.17
with pytest.raises(ValueError) as e:
parser._parse("A", "invalid-cmdline-type")
assert "cmdline_type cannot be" in e.value.args[0]
def test_parse_with_adapter_sequence_as_a_path(tmp_path):
parser = AdapterParser()
with pytest.raises(InvalidCharacter):
parser._parse("invalid.character", "back")
# user forgot to write "file:"
path = (tmp_path / "afile.fasta")
path.write_text(">abc\nACGT\n")
with pytest.raises(InvalidCharacter) as e:
list(parser.parse(str(path), "back"))
assert "A file exists named" in e.value.args[0]
def test_parse_with_parameters():
parser = AdapterParser(
max_error_rate=0.2, min_overlap=4, read_wildcards=False,
adapter_wildcards=False, indels=False)
a = parser._parse('ACGTACGT; e=0.15', 'front')
assert a.max_error_rate == 0.15
assert a.min_overlap == 4
a = parser._parse('ACGTAAAA; o=5; e=0.11', 'back')
assert a.max_error_rate == 0.11
assert a.min_overlap == 5
for spec in ('thename=ACG;e=0.15 ... TGT;e=0.17', 'thename=ACG;e=0.15...TGT;e=0.17'):
a = parser._parse(spec, 'back')
assert isinstance(a, LinkedAdapter)
assert a.front_adapter.max_error_rate == 0.15
assert a.back_adapter.max_error_rate == 0.17