def test_no_collapse_real_data(self):
positions = pd.read_csv("testFiles/testAssignRegions.csv")
arms = HT.get_arms_hg19()
cooler_file = cooler.Cooler(
"testFiles/test3_realdata.mcool::resolutions/50000")
expected = HT.get_expected(cooler_file, arms)
result = HT.do_pileup_obs_exp(cooler_file,
expected,
positions,
proc=1,
collapse=False)
expected = np.load(
"testFiles/real_data_obsexp_pileup_not_collapsed.npy")
self.assertTrue(np.allclose(result, expected, equal_nan=True))
def test_collapse(self):
"""Tests pileup of synthetic Hi-C data, with collapsing results."""
position_frame = pd.read_csv("testFiles/posPileups.csv")
arms = pd.DataFrame({
"chrom": "chrSyn",
"start": 0,
"end": 4990000
},
index=[0])
assigned = HT.assign_regions(50000, 10000, position_frame["chrom"],
position_frame["pos"], arms)
cooler_file = cooler.Cooler(
"testFiles/test2.mcool::/resolutions/10000")
exp_f = HT.get_expected(cooler_file, arms, ignore_diagonals=0)
result = HT.do_pileup_obs_exp(cooler_file,
exp_f,
assigned,
proc=1,
collapse=True)
expected = np.load("testFiles/test_pileups_obsExp_collapse.npy")
self.assertTrue(np.allclose(result, expected))