def test_read_hapmap_nonzero_end(self):
with open(self.temp_file, "w+") as f:
print("HEADER", file=f)
print("chr1 0 5 x", file=f)
print("s 2 1 x x x", file=f)
with pytest.raises(ValueError):
msprime.read_hapmap(self.temp_file)
def test_read_hapmap_nonzero_start(self):
with open(self.temp_file, "w+") as f:
print("HEADER", file=f)
print("chr1 1 5 x", file=f)
print("s 2 0 x x x", file=f)
rm = msprime.read_hapmap(self.temp_file)
np.testing.assert_array_equal(rm.position, [0, 1, 2])
np.testing.assert_array_equal(rm.rate, [0, 5e-8])
def test_read_hapmap_gzipped(self):
try:
filename = self.temp_file + ".gz"
with gzip.open(filename, "w+") as f:
f.write(b"HEADER\n")
f.write(b"chr1 0 1\n")
f.write(b"chr1 1 5.5\n")
f.write(b"s 2 0\n")
rm = msprime.read_hapmap(filename)
np.testing.assert_array_equal(rm.position, [0, 1, 2])
np.testing.assert_array_equal(rm.rate, [1e-8, 5.5e-8])
finally:
os.unlink(filename)
def test_mean_recombination_rate(self):
# Some quick sanity checks.
recomb_map = msprime.RecombinationMap([0, 1], [1, 0])
mean_rr = recomb_map.mean_recombination_rate
assert mean_rr == 1.0
recomb_map = msprime.RecombinationMap([0, 1, 2], [1, 0, 0])
mean_rr = recomb_map.mean_recombination_rate
assert mean_rr == 0.5
recomb_map = msprime.RecombinationMap([0, 1, 2], [0, 0, 0])
mean_rr = recomb_map.mean_recombination_rate
assert mean_rr == 0.0
# Test mean_recombination_rate is correct after reading from
# a hapmap file. read_hapmap() ignores the cM
# field, so here we test against using the cM field directly.
def hapmap_rr(hapmap_file):
first_pos = 0
with open(hapmap_file) as f:
next(f) # skip header
for line in f:
pos, rate, cM = map(float, line.split()[1:4])
if cM == 0:
first_pos = pos
return cM / 100 / (pos - first_pos)
hapmap = """chr pos rate cM
1 4283592 3.79115663174456 0
1 4361401 0.0664276817058413 0.294986106359414
1 7979763 10.9082897515584 0.535345505591925
1 8007051 0.0976780648822495 0.833010916332456
1 8762788 0.0899929572085616 0.906829844052373
1 9477943 0.0864382908650907 0.971188757364862
1 9696341 4.76495005895746 0.990066707213216
1 9752154 0.0864316558730679 1.25601286485381
1 9881751 0.0 1.26721414815999"""
with tempfile.TemporaryDirectory() as temp_dir:
hapfile = os.path.join(temp_dir, "hapmap.txt")
with open(hapfile, "w") as f:
f.write(hapmap)
recomb_map = msprime.read_hapmap(f.name)
mean_rr = recomb_map.mean_rate
mean_rr2 = hapmap_rr(hapfile)
self.assertAlmostEqual(mean_rr, mean_rr2, places=15)