def test_pattern_detector(matrix):
"""Test if pattern detector exits correctly"""
contact_map = DummyMap(matrix, max_dist=100, detectable_bins=None)
# Gaussian kernel
kernel_matrix = gauss_mat(0, 0, 5, shape=(7, 7)).todense()
kernel_config = {
"max_dist": 100,
"precision": 1,
"max_perc_undetected": 10,
}
kernel_matrix = (kernel_matrix + kernel_matrix.T -
np.diag(np.diag(kernel_matrix)))
cud.pattern_detector(contact_map, kernel_config, kernel_matrix)
def _quantify_sub_mat(data):
"""
This function is dispatched by multiprocessing to
run the quantification pipeline.
"""
sub = data[0][1]
config = data[1]
kernel = data[2]
positions = data[3]
# If there is no pattern on this sub matrix,
# do not scan it.
if positions.shape[0]:
sub.contact_map.create_mat()
# Feed the submatrix to quantification pipeline
patterns, windows = cid.pattern_detector(
sub.contact_map,
config,
kernel,
coords=np.array(positions.loc[:, ["bin1", "bin2"]]),
full=True,
tsvd=config["tsvd"],
)
sub.contact_map.destroy_mat()
else:
patterns = windows = None
return {
"coords": patterns,
"windows": windows,
"chr1": sub.chr1,
"chr2": sub.chr2,
}
def _detect_sub_mat(data):
sub = data[0][1]
config = data[1]
kernel = data[2]
dump = data[3]
chrom_patterns, chrom_windows = cid.pattern_detector(
sub.contact_map, config, kernel, dump
)
return {
"coords": chrom_patterns,
"windows": chrom_windows,
"chr1": sub.chr1,
"chr2": sub.chr2,
}
def _detect_sub_mat(data):
sub = data[0][1]
config = data[1]
kernel = data[2]
dump = data[3]
sub.contact_map.create_mat()
chrom_patterns, chrom_windows = cid.pattern_detector(
sub.contact_map,
config,
kernel,
dump=dump,
full=True,
tsvd=config["tsvd"],
)
sub.contact_map.destroy_mat()
return {
"coords": chrom_patterns,
"windows": chrom_windows,
"chr1": sub.chr1,
"chr2": sub.chr2,
}