def trim_seq(self, start, end):
new = record_processing.trim_sequence(self.record, start, end)
# since func called, alter start/end for these slice checks
if start < 0:
start = 0
if end < 0:
end = len(self.seq)
# check that Bio.Seq slices as expected
assert str(self.record.seq[start:end]) == self.seq[start:end]
# check that the record's seq was sliced
assert str(new.seq) == self.seq[start:end]
# return for further checking
return new
def test_bad_values(self):
# start outside seq
with self.assertRaises(ValueError):
record_processing.trim_sequence(self.record, start=10, end=-1)
# end outside seq
with self.assertRaises(ValueError):
record_processing.trim_sequence(self.record, start=-1, end=20)
# start after end
with self.assertRaises(ValueError):
record_processing.trim_sequence(self.record, start=7, end=4)
def test_no_change(self):
new = record_processing.trim_sequence(self.record, start=-1, end=-1)
assert new.seq == self.record.seq
