def test_hic_genome_subsample(self, path):
"""Check results and error handling of contacts subsampling"""
hic_genome = ccm.HicGenome(path)
with self.assertRaises(ValueError):
hic_genome.subsample(-1)
with self.assertRaises(ValueError):
hic_genome.subsample("a")
original_contacts = hic_genome.matrix.sum()
hic_genome.subsample(0.7)
assert np.isclose(hic_genome.matrix.sum(), 0.7 * original_contacts)
hic_genome = ccm.HicGenome(path)
target_contacts = hic_genome.matrix.sum() * 0.2
hic_genome.subsample(target_contacts)
assert np.isclose(hic_genome.matrix.sum(), target_contacts)
def test_hic_genome(path):
"""Test HicGenome instantiation and matrix splitting with bg2 and cool files"""
# Simple instantiation test: no kernel config, no inter matrices
hic_genome = ccm.HicGenome(path)
hic_genome.make_sub_matrices()
n_chroms = len(hic_genome.clr.chromnames)
assert hic_genome.sub_mats.shape[0] == n_chroms
assert hic_genome.max_dist is None
# Test with inter + kernel
hic_genome = ccm.HicGenome(path, inter=True, kernel_config=ck.loops)
hic_genome.make_sub_matrices()
assert hic_genome.sub_mats.shape[0] == n_chroms**2 - n_chroms
assert hic_genome.max_dist == ck.loops["max_dist"] // hic_genome.clr.binsize
assert hic_genome.largest_kernel == ck.loops["kernels"][0].shape[0]
def test_hic_genome_coords_to_bins(path):
"""Test conversion of bins to genomic coordinates"""
hic_genome = ccm.HicGenome(path)
coords = pd.DataFrame({"chrom": ["chr1", "chr2"], "pos": [150, 4000]})
exp_bins = np.array([0, 131])
obs_bins = hic_genome.coords_to_bins(coords)
assert np.all(exp_bins == obs_bins)
def test_hic_genome_bins_to_coords(path):
"""Test conversion of bins to genomic coordinates"""
hic_genome = ccm.HicGenome(path)
idx = [0, 5, 8]
exp_bins = hic_genome.bins.iloc[idx, :]
obs_bins = hic_genome.bins_to_coords(idx)
assert np.all(exp_bins == obs_bins)
def test_hic_genome_get_sub_mat_pattern(path):
"""Test full matrix to sub matrix bin conversion"""
hic_genome = ccm.HicGenome(path)
dummy_patterns = pd.DataFrame({"bin1": [0, 10, 50], "bin2": [1, 11, 51]})
obs_coords = hic_genome.get_sub_mat_pattern("chr1", "chr1", dummy_patterns)
assert np.all(obs_coords.bin1 == dummy_patterns.bin1)
assert np.all(obs_coords.bin2 == dummy_patterns.bin2)
def test_hic_genome_normalize(path):
"""Test if normalization of HicGenome object yields expected results"""
hic_genome = ccm.HicGenome(path)
valid_bins = preproc.get_detectable_bins(hic_genome.matrix, n_mads=5)
hic_genome.normalize(iterations=100)
filtered_mat = hic_genome.matrix.tocsr()[valid_bins[0], :]
filtered_mat = filtered_mat[:, valid_bins[1]]
bin_sums = preproc.sum_mat_bins(filtered_mat)
assert np.allclose(bin_sums, 1, rtol=0.05)
def contact_map_subsample(self, path):
"""Check results and error handling of contacts subsampling"""
with self.assertRaises(ValueError):
ccm.HicGenome(path, sample=-1)
with self.assertRaises(ValueError):
ccm.HicGenome(path, sample="a")
hic_genome = ccm.HicGenome(path)
hic_genome.make_sub_matrices()
for sub in hic_genome.sub_mats.contact_map:
(s1, e1), (s2, e2) = sub.extent
sub.matrix = sub.clr.matrix(sparse=True, balance=True)[s1:e1,
s2:e2]
sub.matrix.data[np.isnan(sub.matrix.data)] = 0
sub.matrix.eliminate_zeros()
ori_sum = sub.clr.matrix(sparse=True, balance=False)[s1:e1,
s2:e2].sum()
sub.subsample(0.7, balance=False)
breakpoint()
print(0.7 * ori_sum, sub.matrix.sum())
assert np.isclose(int(0.7 * ori_sum), sub.matrix.sum())
def test_hic_genome_normalize(path):
"""Test if normalization of HicGenome object yields expected results"""
hic_genome = ccm.HicGenome(path)
hic_genome.normalize(force_norm=True)
def test_hic_genome_normalize(path):
"""Test if normalization of HicGenome object yields expected results"""
hic_genome = ccm.HicGenome(path)
hic_genome.normalize(norm='raw')
hic_genome.normalize(norm='auto')
