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import os.path as op
import h5py
import numpy as np
import pytest
from _common import cooler_cmp, isolated_filesystem
import cooler
from cooler._reduce import coarsen_cooler, legacy_zoomify, merge_coolers, zoomify_cooler
testdir = op.realpath(op.dirname(__file__))
datadir = op.join(testdir, "data")
@pytest.mark.parametrize(
"path1,path2",
[
(
op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"),
),
(
op.join(datadir, "toy.asymm.2.cool"),
op.join(datadir, "toy.asymm.2.cool")
),
],
)
def test_merge(path1, path2):
with isolated_filesystem():
merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6))
single = cooler.Cooler(path1)
merged = cooler.Cooler("test.cool")
assert (
merged.pixels()["count"][:].sum() == 2 * single.pixels()["count"][:].sum()
)
def test_merge2():
with isolated_filesystem():
path1 = op.join(datadir, "toy.symm.upper.2.cool")
path2 = op.join(datadir, "toy.symm.upper.2.cool")
merge_coolers("test.cool", [path1, path2], mergebuf=3, agg={"count": "mean"})
single = cooler.Cooler(path1)
merged = cooler.Cooler("test.cool")
assert merged.pixels()["count"][:].sum() == single.pixels()["count"][:].sum()
# different resolution
path1 = op.join(datadir, "toy.symm.upper.2.cool")
path2 = op.join(datadir, "toy.symm.upper.4.cool")
with pytest.raises(ValueError):
merge_coolers("test.cool", [path1, path2], mergebuf=3)
# incompatible bins
path1 = op.join(datadir, "toy.symm.upper.var.cool")
path2 = op.join(datadir, "toy.symm.upper.2.cool")
with pytest.raises(ValueError):
merge_coolers("test.cool", [path1, path2], mergebuf=3)
path2 = op.join(datadir, "toy.symm.upper.var.cool")
path1 = op.join(datadir, "toy.symm.upper.2.cool")
with pytest.raises(ValueError):
merge_coolers("test.cool", [path1, path2], mergebuf=3)
# incompatible symmetry
path1 = op.join(datadir, "toy.symm.upper.2.cool")
path2 = op.join(datadir, "toy.asymm.2.cool")
with pytest.raises(ValueError):
merge_coolers("test.cool", [path1, path2], mergebuf=3)
# missing value column
path1 = op.join(datadir, "toy.symm.upper.2.cool")
path2 = op.join(datadir, "toy.symm.upper.2.cool")
with pytest.raises(ValueError):
merge_coolers("test.cool", [path1, path2], mergebuf=3, columns=["missing"])
@pytest.mark.parametrize(
"input_uri,factor,ref_uri",
[
(
op.join(datadir, "toy.symm.upper.2.cool"),
2,
op.join(datadir, "toy.symm.upper.4.cool"),
),
(
op.join(datadir, "toy.asymm.2.cool"),
2,
op.join(datadir, "toy.asymm.4.cool")
),
(
op.join(datadir, "toy.symm.upper.var.cool"),
2,
op.join(datadir, "toy.symm.upper.var2x.cool"),
),
],
)
def test_coarsen(input_uri, factor, ref_uri):
with isolated_filesystem():
kwargs = dict(chunksize=10, nproc=1, columns=None, dtypes=None, agg=None)
coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
cooler_cmp("test.cool", ref_uri)
# custom dtype
kwargs = dict(chunksize=10, nproc=1, columns=None, dtypes={"count": np.float64})
coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
with h5py.File("test.cool", "r") as f:
assert f["pixels/count"].dtype.kind == "f"
# custom aggregator
kwargs = dict(
chunksize=10, nproc=1, columns=None, dtypes=None, agg={"count": "mean"}
)
coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
# parallel
kwargs = dict(chunksize=10, nproc=2, columns=None, dtypes=None, agg=None)
coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
# raise on missing value column
kwargs = dict(chunksize=10, nproc=2, columns=["missing"], dtypes=None, agg=None)
with pytest.raises(ValueError):
coarsen_cooler(input_uri, "test.cool", factor, **kwargs)
def test_coarsen_partitions_correctly():
kwargs = dict(nproc=1, columns=None, dtypes=None, agg=None)
with isolated_filesystem():
f_ref = op.join(datadir, "odd.4.cool")
f_in = op.join(datadir, "odd.1.cool")
coarsen_cooler(f_in, "odd.1.coarsen_4.cool", factor=4, chunksize=2, **kwargs)
pix1 = cooler.Cooler(f_ref).pixels()[:]
pix2 = cooler.Cooler("odd.1.coarsen_4.cool").pixels()[:]
assert len(pix1) == len(pix2)
assert sum(pix2[["bin1_id", "bin2_id"]].duplicated()) == 0
assert np.allclose(pix1, pix2)
def test_zoomify():
kwargs = dict(chunksize=10, nproc=1, columns=None, dtypes=None, agg=None)
with isolated_filesystem():
zoomify_cooler(
op.join(datadir, "toy.asymm.2.cool"),
"test.2.mcool",
resolutions=[4, 8, 16, 32],
**kwargs,
)
for res in [2, 4, 8, 16, 32]:
cooler_cmp(
f"test.2.mcool::resolutions/{res}",
op.join(datadir, f"toy.asymm.{res}.cool"),
)
# include base resolution
zoomify_cooler(
op.join(datadir, "toy.asymm.2.cool"),
"test.2.mcool",
resolutions=[2, 4, 8, 16, 32],
**kwargs,
)
for res in [2, 4, 8, 16, 32]:
cooler_cmp(
f"test.2.mcool::resolutions/{res}",
op.join(datadir, f"toy.asymm.{res}.cool"),
)
# impossible resolution to obtain
with pytest.raises(ValueError):
zoomify_cooler(
op.join(datadir, "toy.asymm.2.cool"),
"test.2.mcool",
resolutions=[4, 5, 32],
**kwargs,
)
def test_legacy_zoomify():
infile = op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")
chunksize = int(10e6)
# n_zooms = 2
n_cpus = 1
with isolated_filesystem():
legacy_zoomify(infile, "test.multires.cool", n_cpus, chunksize)
def test_append_mode():
# merge
path1 = path2 = op.join(datadir, "toy.asymm.2.cool")
out_path = "test.cool"
for append in (True, False):
with isolated_filesystem():
with h5py.File("test.cool", "w") as f:
f.attrs["xxxx"] = True
merge_coolers(
out_path,
[path1, path2],
mergebuf=int(15e6),
mode="a" if append else "w",
)
with h5py.File(out_path, "r") as f:
if append:
assert "xxxx" in f.attrs
else:
assert "xxxx" not in f.attrs
# coarsen
input_path = op.join(datadir, "toy.symm.upper.2.cool")
out_path = "test.cool"
for append in (True, False):
with isolated_filesystem():
with h5py.File("test.cool", "w") as f:
f.attrs["xxxx"] = True
coarsen_cooler(
input_path,
"test.cool",
2,
chunksize=10,
nproc=1,
columns=None,
dtypes=None,
agg=None,
mode="a" if append else "w",
)
with h5py.File(out_path, "r") as f:
if append:
assert "xxxx" in f.attrs
else:
assert "xxxx" not in f.attrs
|
