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_expected_real_data(self):
"""Tests expected counts for real Hi-C data
with multiple chromosomal arms. Known values were
provided and expected counts for each diagonal
calculated."""
arms = HT.get_arms_hg19()
cooler_file = cooler.Cooler(
"testFiles/test3_realdata.mcool::/resolutions/50000")
result = HT.get_expected(
cooler_file, arms, proc=1,
ignore_diagonals=0).drop(columns=["count.sum"])
check = pd.read_csv("testFiles/test_expected_realdata.csv")
# merge regions for new expected format
check.loc[:, "region"] = check.apply(
lambda x: f"{x['chrom']}:{x['start']}-{x['end']}", axis=1)
check_final = (check.drop(
columns=["chrom", "start", "end"])[result.columns].sort_values(
by=["region", "diag"]).reset_index(drop=True))
sorted_result = result.sort_values(by=["region", "diag"]).reset_index(
drop=True)
assert_frame_equal(sorted_result, check_final)
def test_arms(self):
"""Tests whether fetching and generating
of supports for chromosomal arms of hg19 works."""
check = pd.read_csv("./testFiles/arms.csv")
arms = HT.get_arms_hg19()
assert_frame_equal(check, arms)
