def test_score_residues(self):
rule = ASI2("SCORE FROM ( 100G => 10, 101D => 20 )")
expected_residue = repr({Mutation('S100G')})
result = rule.dtree(VariantCalls("S100G R101d"))
self.assertEqual(expected_residue, repr(result.residues))
def test_parse_exception(self):
expected_error_message = (
"Error in ASI2: SCORE FROM ( 10R => 2>!<;0 ) (at char 21), (line:1, col:22)"
)
with self.assertRaises(ParseException) as context:
ASI2("SCORE FROM ( 10R => 2;0 )")
self.assertEqual(expected_error_message, str(context.exception))
def test_parse_exception_multiline(self):
rule = """\
SCORE FROM (
10R => 2;0
)
"""
expected_error_message = (
"Error in ASI2: 10R => 2>!<;0 (at char 25), (line:2, col:13)")
with self.assertRaises(ParseException) as context:
ASI2(rule)
self.assertEqual(expected_error_message, str(context.exception))
def test_stanford_rest(self):
examples = [
"SCORE FROM (65R => 20, 74V => 20, 184VI => 20)",
"151M AND EXCLUDE 69i",
# "69(NOT TDN)",
"215F OR 215Y",
"SCORE FROM (101P => 40, 101E => 30, 101HN => 15, 101Q => 5 )",
"SCORE FROM ( MAX (101P => 40, 101E => 30, 101HN => 15, 101Q => 5 ))",
"(184V AND 115F) => 20"
"3N AND 9N",
"2N OR 9N AND 2N",
"3N AND (2N AND (4N OR 2N))"
]
for ex in examples:
x = ASI2(ex)
self.assertEqual(ex, x.rule)
def test_chained_and(self):
rule = ASI2("""
SCORE FROM(41L => 5, 62V => 5, MAX ( 65E => 10, 65N =>
30, 65R => 45 ), MAX ( 67E => 5, 67G => 5, 67H => 5, 67N => 5, 67S =>
5, 67T => 5, 67d => 30 ), 68d => 15, MAX ( 69G => 10, 69i => 60, 69d =>
15 ), MAX ( 70E => 15, 70G => 15, 70N => 15, 70Q => 15, 70R => 5, 70S
=> 15, 70T => 15, 70d => 15 ), MAX ( 74I => 30, 74V => 30 ), 75I => 5,
77L => 5, 115F => 60, 116Y => 10, MAX ( 151L => 30, 151M => 60 ), MAX(
184I => 15, 184V => 15 ), 210W => 5, MAX ( 215A => 5, 215C => 5, 215D
=> 5, 215E => 5, 215F => 10, 215I => 5, 215L => 5, 215N => 5, 215S =>
5, 215V => 5, 215Y => 10 ), MAX ( 219E => 5, 219N => 5, 219Q => 5, 219R
=> 5 ), (40F AND 41L AND 210W AND 215FY) => 5, (41L AND 210W) => 10,
(41L AND 210W AND 215FY) => 5, (41L AND 44AD AND 210W AND 215FY) => 5,
(41L AND 67EGN AND 215FY) => 5, (67EGN AND 215FY AND 219ENQR) => 5,
(67EGN AND 70R AND 184IV AND 219ENQR) => 20, (67EGN AND 70R AND
219ENQR) => 10, (70R AND 215FY) => 5, (74IV AND 184IV) => 15, (77L AND
116Y AND 151M) => 10, MAX ((210W AND 215ACDEILNSV) => 5, (210W AND
215FY) => 10), MAX ((41L AND 215ACDEILNSV) => 5, (41L AND 215FY) =>
15))
""")
self.assertEqual(rule(add_mutations("40F 41L 210W 215Y")), 65)
self.assertEqual(rule(add_mutations("41L 210W 215F")), 60)
self.assertEqual(rule(add_mutations("40F 210W 215Y")), 25)
self.assertEqual(rule(add_mutations("40F 67G 215Y")), 15)
def test_score_negate(self):
rule = ASI2("SCORE FROM ( NOT 100G => 10, NOT 101SD => 20 )")
self.assertEqual(rule(VariantCalls("100G 101d")), 20)
self.assertEqual(rule(VariantCalls("100S 101S")), 10)
def test_score_from(self):
rule = ASI2("SCORE FROM ( 100G => 10, 101D => 20 )")
self.assertEqual(rule(VariantCalls("100G 101d")), 10)
def test_asi2_compat(self):
q = "SCORE FROM ( 98G => 10, 100I => 40,\
MAX (101P => 40, 101E => 30, 101HN => 15, 101Q => 5) )"
ASI2(q)
def test_score_from_exactly(self):
rule = ASI2("SELECT EXACTLY 1 FROM (2T, 7Y)")
score = rule(VariantCalls("2T 7Y 1G"))
self.assertEqual(0, score)
def test_bool_and(self):
rule = ASI2("1G AND (2T AND 7Y)")
self.assertEqual(rule(VariantCalls("2T 7Y 1G")), True)
self.assertEqual(rule(VariantCalls("2T 7d 1G")), False)
self.assertEqual(rule(VariantCalls("7Y 1G 2T")), True)
def test_atleast_missing(self):
rule = ASI2("SELECT ATLEAST 2 FROM (41L, 67N, 70R, 210W, 215F, 219Q)")
with self.assertRaisesRegex(MissingPositionError,
r'Missing position 70.'):
rule(VariantCalls('41L 67N'))
def test_atleast_false(self):
rule = ASI2("SELECT ATLEAST 2 FROM (41L, 67N, 70R, 210W, 215F, 219Q)")
self.assertFalse(rule(VariantCalls('41L 67d 70d 210d 215d 219d')))
def test_hivdb_rules_parse(self):
folder = os.path.dirname(__file__)
rules_file = os.path.join(folder, 'HIVDB.rules')
for line in open(rules_file):
r = ASI2(line)
self.assertEqual(line, r.rule)
def test_stanford_ex1(self):
ASI2("151M OR 69i")
def test_score_from_max(self):
rule = ASI2("SCORE FROM (MAX (100G => 10, 101D => 20, 102D => 30))")
self.assertEqual(rule(VariantCalls("100G 101D 102d")), 20)
self.assertEqual(rule(VariantCalls("100d 101d 102d")), False)
def test_stanford_ex3(self):
ASI2(
"SELECT ATLEAST 2 AND NOTMORETHAN 2 FROM (41L, 67N, 70R, 210W, 215FY, 219QE)"
)
def test_score_from_max_neg(self):
rule = ASI2("SCORE FROM (MAX (100G => -10, 101D => -20, 102D => 30))")
self.assertEqual(rule(VariantCalls("100G 101D 102d")), -10)
def test_stanford_ex4(self):
ASI2("215FY AND NOT 184VI")
def test_bool_or(self):
rule = ASI2("1G OR (2T OR 7Y)")
self.assertTrue(rule(VariantCalls("1d 2T 7d")))
self.assertFalse(rule(VariantCalls("1d 2d 7d")))
self.assertTrue(rule(VariantCalls("1G 2d 7d")))
def test_select_from_atleast(self):
rule = ASI2("SELECT ATLEAST 2 FROM (2T, 7Y, 3G)")
self.assertTrue(rule(VariantCalls("2T 7Y 3d")))
self.assertFalse(rule(VariantCalls("2T 7d 3d")))
self.assertTrue(rule(VariantCalls("3G 7d 2T")))