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import os.path as op
import shutil
import h5py
from _common import cooler_cmp, isolated_filesystem
from cooler import fileops
import pytest
testdir = op.realpath(op.dirname(__file__))
def test_is_cooler():
assert not fileops.is_cooler(op.join(testdir, "data", "toy.chrom.sizes"))
assert fileops.is_cooler(op.join(testdir, "data", "toy.symm.upper.2.cool"))
assert not fileops.is_cooler(op.join(testdir, "data", "toy.symm.upper.2.mcool"))
assert fileops.is_cooler(
op.join(testdir, "data", "toy.symm.upper.2.mcool") + "::resolutions/2"
)
def test_is_multires_file():
assert not fileops.is_multires_file(op.join(testdir, "data", "toy.chrom.sizes"))
assert not fileops.is_multires_file(
op.join(testdir, "data", "toy.symm.upper.2.cool")
)
assert fileops.is_multires_file(op.join(testdir, "data", "toy.symm.upper.2.mcool"))
def test_list_coolers():
listing = fileops.list_coolers(op.join(testdir, "data", "toy.symm.upper.2.mcool"))
paths = set(listing)
for path in (
"/resolutions/2",
"/resolutions/4",
"/resolutions/8",
"/resolutions/16",
"/resolutions/32",
):
assert path in paths
def test_ls_attr_tree():
src_file = op.join(testdir, "data", "toy.symm.upper.2.mcool")
with h5py.File(src_file, "r") as f:
attr_dict = fileops.read_attr_tree(f, level=None)
assert attr_dict["@attrs"]["format"] == "HDF5::MCOOL"
def test_ls_data_tree():
with isolated_filesystem():
src_file = op.join(testdir, "data", "toy.symm.upper.2.mcool")
listing = fileops.ls(src_file + "::" + "resolutions/2")
for path in [
"/resolutions/2",
"/resolutions/2/chroms",
"/resolutions/2/chroms/name",
"/resolutions/2/chroms/length",
"/resolutions/2/bins",
"/resolutions/2/bins/chrom",
"/resolutions/2/bins/start",
"/resolutions/2/bins/end",
"/resolutions/2/pixels",
"/resolutions/2/pixels/bin1_id",
"/resolutions/2/pixels/bin2_id",
"/resolutions/2/pixels/count",
]:
assert path in listing
def test_cp():
with isolated_filesystem():
src_file = op.join(testdir, "data", "toy.symm.upper.2.mcool")
# file-to-file
src_uri = src_file + "::resolutions/2"
fileops.cp(src_uri, "test.2.cool")
cooler_cmp(src_uri, "test.2.cool")
fileops.cp(src_uri, "test.2.cool::/nested/")
cooler_cmp(src_uri, "test.2.cool::nested")
# within-file
test_file = "test.src.mcool"
shutil.copyfile(src_file, test_file)
fileops.cp(test_file + "::resolutions/2", test_file + "::abc/d")
cooler_cmp(test_file + "::resolutions/2", test_file + "::abc/d")
with h5py.File(test_file, mode="r") as f:
assert "resolutions/2" in f
assert "abc/d" in f
assert f["resolutions/2"].id != f["abc/d"].id
def test_mv():
with isolated_filesystem():
ref_file = "test.ref.mcool"
src_file = "test.src.mcool"
shutil.copyfile(op.join(testdir, "data", "toy.symm.upper.2.mcool"), ref_file)
shutil.copyfile(op.join(testdir, "data", "toy.symm.upper.2.mcool"), src_file)
fileops.mv(src_file + "::resolutions/2", src_file + "::abc/d")
with h5py.File(src_file, mode="r") as f:
assert "resolutions/2" not in f
assert "abc/d" in f
cooler_cmp(ref_file + "::resolutions/2", src_file + "::abc/d")
def test_ln():
with isolated_filesystem():
src_file = op.join(testdir, "data", "toy.symm.upper.2.mcool")
# within-file hard link
test_file = "test.hardlink.mcool"
shutil.copyfile(src_file, test_file)
fileops.ln(test_file + "::resolutions/2", test_file + "::abc/d")
with h5py.File(test_file, mode="r") as f:
assert "resolutions/2" in f
assert "abc/d" in f
assert f["resolutions/2"].id == f["abc/d"].id
cooler_cmp(test_file + "::resolutions/2", test_file + "::abc/d")
# within-file soft link
test_file = "test.softlink.mcool"
shutil.copyfile(src_file, test_file)
fileops.ln(test_file + "::resolutions/2", test_file + "::abc/d", soft=True)
with h5py.File(test_file, mode="r") as f:
assert "resolutions/2" in f
assert "abc/d" in f
assert f["resolutions/2"].id == f["abc/d"].id
cooler_cmp(test_file + "::resolutions/2", test_file + "::abc/d")
# between-file external link
test_file = "test.extlink.mcool"
dst_file = "test.dst.cool"
shutil.copyfile(src_file, test_file)
fileops.ln(test_file + "::resolutions/2", dst_file + "::abc/d", soft=True)
cooler_cmp(test_file + "::resolutions/2", dst_file + "::abc/d")
@pytest.mark.skip("Test needs ipytree which is not yet packaged for Debian ... skipped")
def test_print_trees():
src_file = op.join(testdir, "data", "toy.symm.upper.2.mcool")
fileops.pprint_attr_tree(src_file, level=3)
fileops.pprint_data_tree(src_file, level=3)
with h5py.File(src_file) as f:
t = fileops.TreeViewer(f)
t._repr_mimebundle_()
def test_is_scool_file():
src_file = op.join(testdir, "data", "scool_test_file.scool")
assert fileops.is_scool_file(src_file)
def test_list_scool_cells():
src_file = op.join(testdir, "data", "scool_test_file.scool")
paths = [
"/cells/GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool",
"/cells/GSM2687249_41670_GGCTAC-R1-DpnII.100000.cool",
"/cells/GSM2687250_41671_TTAGGC-R1-DpnII.100000.cool",
"/cells/GSM2687251_41672_AGTTCC-R1-DpnII.100000.cool",
"/cells/GSM2687252_41673_CCGTCC-R1-DpnII.100000.cool",
]
cell_paths = fileops.list_scool_cells(src_file)
assert len(cell_paths) == 5
assert all([cell in paths for cell in cell_paths])
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