def test_region_spans_multiple_supports(self):
"""Tests assign regions when region spans multiple supports."""
bed_file = pd.read_csv("testFiles/multiple_support_regions.csv")
result = HT.assign_regions(
window=1000000,
binsize=20000,
chroms=bed_file["chrom"],
positions=bed_file["pos"],
arms=self.arms,
)
expected = pd.read_csv("testFiles/multiple_support_regions_result.csv")
assert_series_equal(result["region"], expected["region"])
def test_case1(self):
"""Test assignment of small, synthetic set of regions."""
bed_file = pd.read_csv("testFiles/testSmall.bed", sep="\t")
result = HT.assign_regions(
window=500000,
binsize=50000,
chroms=bed_file["chrom"],
positions=bed_file["pos"],
arms=self.arms,
)
expected = pd.read_csv("testFiles/testAssignRegions.csv")
assert_frame_equal(result, expected)
def test_regions_are_close_to_supports(self):
"""Tests assign regions when regions are close to supports -> bug was found"""
bed_file = pd.read_csv(
"testFiles/regions_close_to_support_boundary.tsv", sep="\t")
result = HT.assign_regions(
window=1000000,
binsize=20000,
chroms=bed_file["chrom"],
positions=bed_file["pos"],
arms=self.arms,
)
expected = pd.read_csv(
"testFiles/regions_close_to_support_boundary_result.tsv",
delim_whitespace=True,
)
assert_series_equal(result["region"], expected["region"])
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")
result = HT.do_pileup_iccf(cooler_file,
assigned,
proc=1,
collapse=True)
expected = np.load("testFiles/test_pileups_iccf_collapse.npy")
self.assertTrue(np.allclose(result, expected))