def test_genome_wide_norm(self):
"""Tests functionality to extract Obs/Exp values
genome-wide with median normalization from synthetic Hi-C data."""
position_frame = pd.read_csv("testFiles/posPileups.csv")
position_frame.loc[:, "mid"] = position_frame["pos"]
arms = pd.DataFrame({
"chrom": "chrSyn",
"start": 0,
"end": 4990000
},
index=[0])
cooler_file = cooler.Cooler(
"testFiles/test2.mcool::/resolutions/10000")
exp_f = HT.get_expected(cooler_file, arms, ignore_diagonals=0)
pairing_score = HT.get_pairing_score_obs_exp(cooler_file,
exp_f,
50000,
arms=arms,
norm=True)
expected = pd.read_csv(
"testFiles/test_pairingScore_obsExp_genomeWide_Norm.csv",
dtype={
name: pairing_score.dtypes[name]
for name in pairing_score.dtypes.index
},
)
assert_frame_equal(pairing_score, expected)
def test_specific_regions(self):
"""Tests functionality to extract Obs/Exp values
at specific regions from synthetic Hi-C data."""
position_frame = pd.read_csv("testFiles/posPileups.csv")
position_frame.loc[:, "mid"] = position_frame["pos"]
arms = pd.DataFrame({
"chrom": "chrSyn",
"start": 0,
"end": 4990000
},
index=[0])
cooler_file = cooler.Cooler(
"testFiles/test2.mcool::/resolutions/10000")
exp_f = HT.get_expected(cooler_file, arms, ignore_diagonals=0)
pairing_score = HT.get_pairing_score_obs_exp(cooler_file,
exp_f,
50000,
regions=position_frame,
arms=arms,
norm=False)
expected = pd.read_csv(
"testFiles/test_pairingScore_obsExp_specificRegions.csv")
assert_frame_equal(pairing_score, expected)
