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import pytest
from dnaio import SequenceRecord
class TestSequenceRecord:
def test_too_many_qualities(self):
with pytest.raises(ValueError):
SequenceRecord(name="name", sequence="ACGT", qualities="#####")
def test_fastq_bytes(self):
assert (
SequenceRecord("name", "ACGT", "====").fastq_bytes()
== b"@name\nACGT\n+\n====\n"
)
def test_fastq_bytes_two_headers(self):
assert (
SequenceRecord("name", "ACGT", "====").fastq_bytes(two_headers=True)
== b"@name\nACGT\n+name\n====\n"
)
def test_is_mate_succes(self):
assert SequenceRecord("name1", "A", "=").is_mate(
SequenceRecord("name2", "GC", "FF")
)
def test_reverse_complement(self):
assert SequenceRecord(
"name1",
"ACGTUMRWSYKVHDBNacgtumrwsykvhdbn",
"/AAAA/6E/EEEEEEEEEEEE/EEEEA///E/",
).reverse_complement() == SequenceRecord(
"name1",
"nvhdbmrswykaacgtNVHDBMRSWYKAACGT",
"/E///AEEEE/EEEEEEEEEEEE/E6/AAAA/",
)
def test_reverse_complement_none_qualities(self):
assert SequenceRecord(
"name1", "GATTACA", None
).reverse_complement() == SequenceRecord("name1", "TGTAATC", None)
def test_init_name_bad(self):
with pytest.raises(ValueError) as error:
SequenceRecord("nąme1", "A", "=")
error.match("ASCII")
def test_init_name_none(self):
with pytest.raises(TypeError) as error:
SequenceRecord(None, "A", "=")
error.match("str")
def test_init_sequence_bad(self):
with pytest.raises(ValueError) as error:
SequenceRecord("name1", "Ä", "=")
error.match("ASCII")
def test_init_sequence_none(self):
with pytest.raises(TypeError) as error:
SequenceRecord("name1", None, "=")
error.match("str")
def test_init_qualities_bad(self):
with pytest.raises(ValueError) as error:
SequenceRecord("name1", "A", "ä")
error.match("ASCII")
def test_init_qualities_none(self):
seq = SequenceRecord("name1", "A", None)
assert seq.qualities is None
def test_set_name_bad(self):
seq = SequenceRecord("name1", "A", "=")
with pytest.raises(ValueError) as error:
seq.name = "näme1"
error.match("ASCII")
def test_set_name_none(self):
seq = SequenceRecord("name1", "A", "=")
with pytest.raises(TypeError) as error:
seq.name = None
error.match("str")
def test_set_sequence_bad(self):
seq = SequenceRecord("name1", "A", "=")
with pytest.raises(ValueError) as error:
seq.sequence = "Ä"
error.match("ASCII")
def test_set_sequence_none(self):
seq = SequenceRecord("name1", "A", "=")
with pytest.raises(TypeError) as error:
seq.sequence = None
error.match("str")
def test_set_qualities_bad(self):
seq = SequenceRecord("name1", "A", "=")
with pytest.raises(ValueError) as error:
seq.qualities = "Ä"
error.match("ASCII")
def test_set_qualities_none(self):
seq = SequenceRecord("name1", "A", "=")
seq.qualities = None
assert seq.qualities is None
def test_set_id(self):
seq = SequenceRecord("name", "A", "=")
with pytest.raises(AttributeError):
seq.id = "Obi-Wan"
def test_set_comment(self):
seq = SequenceRecord("name", "A", "=")
with pytest.raises(AttributeError):
seq.comment = "Hello there!"
@pytest.mark.parametrize(
["record", "expected"],
[
(SequenceRecord("name", "A", "="), None),
(SequenceRecord("name ", "A", "="), None),
(SequenceRecord("name ", "A", "="), None),
(SequenceRecord("name", "A", "="), None),
(SequenceRecord("AotC I hate sand!", "A", "="), "I hate sand!"),
(
SequenceRecord("Givemesome space", "A", "="),
"space",
),
],
)
def test_get_comment(self, record, expected):
assert record.comment == expected
@pytest.mark.parametrize(
["record", "expected"],
[
(SequenceRecord("name", "A", "="), "name"),
(SequenceRecord("name ", "A", "="), "name"),
(SequenceRecord("name ", "A", "="), "name"),
(SequenceRecord("name", "A", "="), "name"),
(SequenceRecord("AotC I hate sand!", "A", "="), "AotC"),
],
)
def test_get_id(self, record, expected):
assert record.id == expected
def test_reset_id_and_comment_on_name_update(self):
record = SequenceRecord("Obi-Wan: don't try it!", "", "")
assert record.id == "Obi-Wan:"
assert record.comment == "don't try it!"
record.name = "Anakin: you underestimate my power!"
assert record.id == "Anakin:"
assert record.comment == "you underestimate my power!"
def test_legacy_sequence():
from dnaio import Sequence
s = Sequence("name", "ACGT", "####")
assert isinstance(s, SequenceRecord)
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