def test__get_neighbor_directions():
direction_dict = {
(0, 0): 0,
(1, 1): 0,
(2, 2): 0,
(3, 3): 0,
(0, 1): 1,
(1, 0): -1,
(0, 2): 1,
(2, 0): -1,
(1, 3): 1,
(3, 1): -1,
(2, 3): 1,
(3, 2): -1
}
gpm = GenotypePhenotypeMap(["00", "01", "10", "11"])
gpm.get_neighbors()
for i in range(len(gpm.neighbors)):
edge = gpm.neighbors.edge[i]
dir = gpm.neighbors.direction[i]
assert direction_dict[edge] == dir
# Flip map, should flip directions except 0
gpm.wildtype = "11"
for i in range(len(gpm.neighbors)):
edge = gpm.neighbors.edge[i]
dir = gpm.neighbors.direction[i]
assert direction_dict[edge] == -dir
def test_wildtype_setter(test_data):
"""
This is a complicated setter that triggers recalcuation of the binary
map.
"""
for d in test_data:
gpm = GenotypePhenotypeMap(wildtype=d["wildtype"],
genotype=d["genotype"])
# Trivial set (should not change)
gpm.wildtype = d["wildtype"]
assert np.array_equal(gpm.binary, d["binary"])
assert gpm.mutant == d["mutant"]
# Something with wrong dimension
with pytest.raises(ValueError):
gpm.wildtype = "1"
# Feed in something that can't be interpreted as iterable
with pytest.raises(ValueError):
gpm.wildtype = 0
# Feed in something with wrong dimension
with pytest.raises(ValueError):
gpm.wildtype = []
# Feed in genotype with states not seen in the test datasets
with pytest.raises(ValueError):
gpm.wildtype = "".join(["Z" for _ in range(len(gpm.wildtype))])
# Feed in wildtype as list, not str
with pytest.raises(ValueError):
gpm.wildtype = [s for s in gpm.wildtype]
# Should work
gpm.wildtype = d["mutant"]
# Check that wildtype actually fhanged
assert gpm.wildtype == d["mutant"]
# Check mutant (should differ at all variable sites)
for i in range(len(gpm.wildtype)):
if len(d["mutations"][i]) != 1:
assert gpm.mutant[i] != gpm.wildtype[i]
# Make sure n_mutations has flipped properly.
for i in range(len(gpm.genotype)):
counts = sum([
1 for j in range(len(gpm.genotype[i]))
if gpm.genotype[i][j] != gpm.wildtype[j]
])
assert gpm.n_mutations[i] == counts
# Check to make sure the binary was recalculated. This tests whether
# the encoding table and binary are different from before. Does *not*
# check accuracy. This check is done in the
# test_utils.test_genotypes_to_binary function.
binary = utils.genotypes_to_binary(gpm.genotype, gpm.encoding_table)
assert np.array_equal(binary, gpm.binary)
assert not np.array_equal(binary, d["binary"])