def test_from_file_mismatch_0(self):
"""Read barcodes from file, no mismatches.
Result: file 1, 3 and UNKNOWN contain one read, file 4 contains two.
"""
demux([self._input], self._barcodes, False, None, None, None, 0, True)
assert len(self._handles) == 4
assert self._md5_check('./demultiplex_UNKNOWN.fq',
'7a2889d04b4e8514ca01ea6c75884cd6')
def test_from_file_mismatch_1(self):
"""Read barcodes from file, one mismatch.
Result: file 1-3 contain one read, file 4 contains two and UNKNOWN is
empty. Notably file 2 is not empty although the barcode is shorter.
"""
demux([self._input], self._barcodes, False, None, None, None, 1, True)
assert len(self._handles) == 4
assert self._md5_check('./demultiplex_2.fq',
'7a2889d04b4e8514ca01ea6c75884cd6')
def test_x_from_file_mismatch_0(self):
"""Read barcodes from file, no mismatches, HiSeq X headers.
Result: file 1-3 contain one sequence, file 4 contains two and UNKNOWN
is empty.
"""
demux([self._input_x], self._barcodes, False, None, None, None, 0,
True)
assert len(self._handles) == 4
assert self._md5_check('./demultiplex_x_1.fq',
'3f013cddfedf1b5b1ad5d01913692333')
assert self._md5_check('./demultiplex_x_4.fq',
'a044932ca48decaba985032ecf725753')
def test_wrong_barcode_format(self):
handle = make_fake_file('', 'ACTA\nACTC\nACTG\nACTT\n')
try:
demux([self._input], handle, False, None, None, None, 0, False)
except ValueError as error:
assert str(error) == 'invalid barcodes file format'