# Copyright 2018 Google LLC.
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"""Tests for cigar."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import itertools
from absl.testing import absltest
from absl.testing import parameterized
from third_party.nucleus.protos import cigar_pb2
from third_party.nucleus.util import cigar
_CIGAR_TUPLES_AND_CIGAR_UNITS = [
((1, 'M'),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.ALIGNMENT_MATCH, operation_length=1)),
((2, 'I'),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.INSERT, operation_length=2)),
((3, 'D'),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.DELETE, operation_length=3)),
((4, 'N'),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.SKIP, operation_length=4)),
((5, 'S'),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.CLIP_SOFT, operation_length=5)),
((6, 'H'),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.CLIP_HARD, operation_length=6)),
((7, 'P'),
cigar_pb2.CigarUnit(operation=cigar_pb2.CigarUnit.PAD,
operation_length=7)),
((8, '='),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.SEQUENCE_MATCH, operation_length=8)),
((9, 'X'),
cigar_pb2.CigarUnit(
operation=cigar_pb2.CigarUnit.SEQUENCE_MISMATCH, operation_length=9)),
]
def _example_cigar_string_and_units(repeat=3):
examples = {}
for x in itertools.product(_CIGAR_TUPLES_AND_CIGAR_UNITS, repeat=repeat):
lengths_and_opstrs, cigar_units = zip(*x)
cigar_str = ''.join(str(l) + opstr for l, opstr in lengths_and_opstrs)
examples[cigar_str] = list(cigar_units)
return examples
class CigarTests(parameterized.TestCase):
@parameterized.parameters((cigar_units, cigar_str)
for cigar_str, cigar_units in
_example_cigar_string_and_units(3).items())
def test_format_cigar_units(self, cigar_units, expected):
self.assertEqual(cigar.format_cigar_units(cigar_units), expected)
@parameterized.parameters(
('10M', 10),
('10=', 10),
('10X', 10),
('10M2I3M', 13),
('10M2D3M', 15),
('10M2N3M', 15),
('1S10M2D3M', 15),
('1S10M2D3M1S', 15),
('1S10M2D3M1S5H', 15),
('8H1S10M2D3M1S5H', 15),
('8H1S10M2N3M1S5H', 15),
)
def test_alignment_length(self, cigar_str, expected):
cigar_units = cigar.parse_cigar_string(cigar_str)
self.assertEqual(cigar.alignment_length(cigar_units), expected)
@parameterized.parameters(
(length, opstr, expected)
for (length, opstr), expected in _CIGAR_TUPLES_AND_CIGAR_UNITS)
def test_to_cigar_unit(self, length, opstr, expected):
# Check we can convert a tuple and list of length and opstr.
self.assertEqual(cigar.to_cigar_unit((length, opstr)), expected)
self.assertEqual(cigar.to_cigar_unit([length, opstr]), expected)
# Check that we can convert a string version len+opstr.
self.assertEqual(cigar.to_cigar_unit(str(length) + opstr), expected)
# Check that we can pass a CigarUnit through without modification.
self.assertEqual(cigar.to_cigar_unit(expected), expected)
# Check that we can pass length as a string.
self.assertEqual(cigar.to_cigar_unit((str(length), opstr)), expected)
@parameterized.parameters(
'-1M',
'0M',
'',
'M',
'M12',
'4m',
# Have to be wrapped in a list to stop parameterized from treating the
# tuple as the positional arguments to the test function.
[()],
[(4)],
[(4, 'M', 'X')],
[(4, 'M', 10)],
[{4, 'M'}],
# This integer is too large to fit in an int64 cigar, make sure an
# exception is thrown. Max int64 is 9,223,372,036,854,775,807, so we try
# one more.
'9223372036854775808M',
)
def test_to_cigar_unit_detects_bad_args(self, bad):
with self.assertRaises(ValueError):
cigar.to_cigar_unit(bad)
@parameterized.parameters(
list(zip(*to_convert))
for to_convert in itertools.product(
_CIGAR_TUPLES_AND_CIGAR_UNITS, repeat=3))
def test_to_cigar_units(self, to_convert, expected):
# We can convert the raw form.
to_convert = list(to_convert)
expected = list(expected)
actual = cigar.to_cigar_units(to_convert)
self.assertEqual(actual, expected)
# We can also convert the string form by formatting actual.
self.assertEqual(
cigar.to_cigar_units(cigar.format_cigar_units(actual)), expected)
@parameterized.parameters(
(str(length) + opstr, [expected])
for (length, opstr), expected in _CIGAR_TUPLES_AND_CIGAR_UNITS)
def test_parse_cigar_string_single(self, cigar_str, expected):
self.assertEqual(cigar.parse_cigar_string(cigar_str), expected)
@parameterized.parameters(_example_cigar_string_and_units(3).items())
def test_parse_cigar_string_three_pieces(self, cigar_str, expected):
self.assertEqual(cigar.parse_cigar_string(cigar_str), expected)
@parameterized.parameters(
'',
'12',
'12m',
'12?',
'M12',
'12M1',
'12MI',
'12M-1I',
'12.0M',
)
def test_parse_cigar_string_detects_bad_inputs(self, bad_cigar_str):
with self.assertRaises(ValueError):
cigar.parse_cigar_string(bad_cigar_str)
if __name__ == '__main__':
absltest.main()
