def test_parse_file_notation(tmpdir):
tmp_path = str(tmpdir.join('adapters.fasta'))
with open(tmp_path, 'w') as f:
f.write(
dedent(""">first_name
ADAPTER1
>second_name
ADAPTER2
"""))
parser = AdapterParser(max_error_rate=0.2,
min_overlap=4,
read_wildcards=False,
adapter_wildcards=False,
indels=False)
adapters = list(parser.parse('file:' + tmp_path, cmdline_type='back'))
assert len(adapters) == 2
assert adapters[0].name == 'first_name'
assert adapters[0].sequence == 'ADAPTER1'
assert adapters[1].name == 'second_name'
assert adapters[1].sequence == 'ADAPTER2'
for a in adapters:
assert a.max_error_rate == 0.2
assert a.min_overlap == 4
assert not a.read_wildcards
assert not a.adapter_wildcards
assert not a.indels
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_anywhere_parameter_front():
parser = AdapterParser(max_error_rate=0.2, min_overlap=4, read_wildcards=False,
adapter_wildcards=False, indels=True)
adapter = list(parser.parse('CTGAAGTGAAGTACACGGTT;anywhere', 'front'))[0]
assert isinstance(adapter, FrontAdapter)
assert adapter._force_anywhere
# TODO move the rest to a separate test
read = Sequence('foo1', 'AAAAAAAAAACTGAAGTGAA')
from cutadapt.modifiers import AdapterCutter
cutter = AdapterCutter([adapter])
trimmed_read = cutter(read, ModificationInfo(read))
assert trimmed_read.sequence == ''
def test_anywhere_parameter():
parser = AdapterParser(max_error_rate=0.2,
min_overlap=4,
read_wildcards=False,
adapter_wildcards=False,
indels=True)
adapter = list(parser.parse('CTGAAGTGAAGTACACGGTT;anywhere', 'back'))[0]
assert adapter.remove == 'suffix'
assert adapter.where is Where.ANYWHERE
read = Sequence('foo1', 'TGAAGTACACGGTTAAAAAAAAAA')
from cutadapt.modifiers import AdapterCutter
cutter = AdapterCutter([adapter])
trimmed_read = cutter(read, [])
assert trimmed_read.sequence == ''