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from unittest import mock
import numpy as np
import pytest
from scipy import sparse
class MockGroup(dict):
file = mock.Mock(["mode"])
attrs = mock.MagicMock(dict)
def __getitem__(self, path):
current_item = self
if set(path) == {"/"}:
return self
for item in path.split("/"):
current_item = dict.__getitem__(current_item, item)
return current_item
def __setitem__(self, path, value):
if isinstance(value, dict):
value = MockGroup()
# else:
# value = mock.Mock(h5py.Dataset)
current_item = self
previous_item = None
for item in path.split("/"):
previous_item = current_item
try:
current_item = dict.__getitem__(current_item, item)
except KeyError:
dict.__setitem__(current_item, item, MockGroup())
current_item = dict.__getitem__(current_item, item)
dict.__setitem__(previous_item, item, value)
def __delitem__(self, path):
current_item = self
previous_item = None
for item in path.split("/"):
previous_item = current_item
current_item = dict.__getitem__(current_item, item)
dict.__delitem__(previous_item, item)
class MockCooler(MockGroup):
@classmethod
def make_random(cls, chrom_offsets, binsize, density):
chrom_nbins = np.diff(chrom_offsets)
assert chrom_offsets[0] == 0 and np.all(np.diff(chrom_offsets) >= 0)
n_chroms = len(chrom_offsets) - 1
n_bins = chrom_offsets[-1]
chroms = {
"name": np.array(
["chr" + str(i) for i in range(1, n_chroms + 1)], dtype="S"
),
"length": np.array(
[chrom_nbins[i] * binsize for i in range(n_chroms)], dtype=np.int32
),
}
bins = {
"chrom": np.concatenate([[i] * chrom_nbins[i] for i in range(n_chroms)]),
"start": np.concatenate(
[
np.arange(0, chrom_nbins[i] * binsize, binsize)
for i in range(n_chroms)
]
),
"end": np.concatenate(
[
np.arange(binsize, chrom_nbins[i] * (binsize + 1), binsize)
for i in range(n_chroms)
]
),
}
r = sparse.random(n_bins, n_bins, density=density, random_state=1)
r = sparse.triu(r, k=1).tocsr()
pixels = {"bin1_id": r.tocoo().row, "bin2_id": r.indices, "count": r.data}
indexes = {
"chrom_offset": np.array(chrom_offsets, dtype=np.int32),
"bin1_offset": r.indptr,
}
return cls(chroms, bins, pixels, indexes, binsize)
def __init__(self, chroms, bins, pixels, indexes, binsize):
self.file = self
self.file.mode = "r"
self.file.filename = "mock.cool"
self.name = "/"
self.attrs = {
"bin-size": binsize,
"bin-type": "fixed",
"symmetric-storage-mode": "upper",
"nchroms": len(chroms),
"nbins": len(bins["chrom"]),
"nnz": len(pixels["bin1_id"]),
"metadata": "{}",
}
super().__init__(
{"chroms": chroms, "bins": bins, "pixels": pixels, "indexes": indexes}
)
@pytest.fixture(params=[([0, 10, 20], 100, 1)])
def mock_cooler(request):
chrom_offsets, binsize, density = request.param
return MockCooler.make_random(chrom_offsets, binsize, density)
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