def test_removal(self):
record = Record(Seq("acg-ta--"))
record = record_processing.sanitise_sequence(record)
assert record.seq == "ACGTA"
# test modified in place
record = Record(Seq("acg-ta--"))
record_processing.sanitise_sequence(record)
assert record.seq == "ACGTA"
def test_no_conversion_required(self):
gaps = "acgtNacgtN"
no_gaps = "acgtacgt"
records = [Record(Seq(gaps)), Record(Seq(no_gaps))]
records = [record_processing.sanitise_sequence(record) for record in records]
assert len(records) == 2
assert records[0].seq == gaps.upper()
assert records[1].seq == no_gaps.upper()
def test_conversion(self):
for seq in ("acgtZacgtX", "acgtxacgtz", "acgtoacgtf"):
record = Record(Seq(seq))
record = record_processing.sanitise_sequence(record)
assert record.seq == "ACGTNACGTN"
def test_mix(self):
record = Record(Seq("acg-ta-F-x"))
record = record_processing.sanitise_sequence(record)
assert record.seq == "ACGTANN"