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import os.path as op
import numpy as np
import pandas as pd
from click.testing import CliRunner
import cooler
### COMPUTE ###
from cooler.cli.balance import balance
from cooler.cli.coarsen import coarsen
## REDUCTION ###
from cooler.cli.merge import merge
from cooler.cli.zoomify import zoomify
# import pytest
testdir = op.realpath(op.dirname(__file__))
datadir = op.join(testdir, "data")
def test_merge():
runner = CliRunner()
with runner.isolated_filesystem():
f_in = op.join(datadir, "toy.symm.upper.2.cool")
result = runner.invoke(
merge, ["toy.2.double.cool", f_in, f_in, "--field", "count:dtype=int"]
)
assert result.exit_code == 0
total1 = cooler.Cooler(f_in).pixels()["count"][:].sum()
total2 = cooler.Cooler("toy.2.double.cool").pixels()["count"][:].sum()
assert total2 == 2 * total1
def test_coarsen():
runner = CliRunner()
with runner.isolated_filesystem():
f_in = op.join(datadir, "toy.symm.upper.2.cool")
f_ref = op.join(datadir, "toy.symm.upper.4.cool")
result = runner.invoke(
coarsen,
[f_in, "--factor", "2", "--nproc", "2", "-o", "toy.2.coarsen_2.cool"],
)
assert result.exit_code == 0
pix1 = cooler.Cooler(f_ref).pixels()["count"][:]
pix2 = cooler.Cooler("toy.2.coarsen_2.cool").pixels()["count"][:]
assert np.allclose(pix1, pix2)
result = runner.invoke(
coarsen,
[
f_in,
"--factor",
"2",
"--field",
"count:dtype=float,agg=mean",
"-o",
"toy.2.coarsen_2_mean.cool",
],
)
assert result.exit_code == 0
pix2 = cooler.Cooler("toy.2.coarsen_2_mean.cool").pixels()["count"][:]
assert pix2.dtype.kind == "f"
def test_zoomify():
runner = CliRunner()
with runner.isolated_filesystem():
f_in = op.join(datadir, "toy.symm.upper.2.cool")
result = runner.invoke(
zoomify, [f_in, "--balance", "--legacy", "-o", "toy.2.mcool"]
)
assert result.exit_code == 0
f_in = op.join(datadir, "toy.symm.upper.2.cool")
result = runner.invoke(
zoomify, [f_in, "--balance", "--nproc", "2", "-o", "toy.2.mcool"]
)
assert result.exit_code == 0
f_in = op.join(datadir, "toy.symm.upper.2.cool")
result = runner.invoke(
zoomify, [f_in, "--balance", "--resolutions", "2,4,8", "-o", "toy.2.mcool"]
)
assert result.exit_code == 0
f_in = op.join(datadir, "toy.symm.upper.2.cool")
result = runner.invoke(
zoomify,
[
f_in,
"--balance",
"--resolutions",
"2,4,8",
"--field",
"count:dtype=float,agg=mean",
"-o",
"toy.2.mcool",
],
)
assert result.exit_code == 0
# pix1 = cooler.Cooler(f_ref).pixels()['count'][:]
# pix2 = cooler.Cooler('toy.4.cool').pixels()['count'][:]
# assert np.allclose(pix1, pix2)
def test_balance():
runner = CliRunner()
with runner.isolated_filesystem():
f_in = op.join(datadir, "toy.symm.upper.2.cool")
result = runner.invoke(
balance,
[
f_in,
"--ignore-diags",
"2",
"--mad-max",
"0",
"--min-nnz",
"0",
"--tol",
"0.05",
"--nproc",
"2",
"--stdout",
],
)
assert result.exit_code == 0
assert len(result.output.split("\n")) == 32
# convergence
result = runner.invoke(
balance,
[
f_in,
"--ignore-diags",
"2",
"--mad-max",
"0",
"--min-nnz",
"0",
"--tol",
"0.05",
"--max-iters",
"1",
"--convergence-policy",
"store_final",
"--stdout",
],
)
assert result.exit_code == 0
assert len(result.output)
result = runner.invoke(
balance,
[
f_in,
"--ignore-diags",
"2",
"--mad-max",
"0",
"--min-nnz",
"0",
"--tol",
"0.05",
"--max-iters",
"1",
"--convergence-policy",
"discard",
"--stdout",
],
)
assert result.exit_code == 0
assert not result.output
result = runner.invoke(
balance,
[
f_in,
"--ignore-diags",
"2",
"--mad-max",
"0",
"--min-nnz",
"0",
"--tol",
"0.05",
"--max-iters",
"1",
"--convergence-policy",
"error",
"--stdout",
],
)
assert result.exit_code == 1
# file is unbalanced
result = runner.invoke(
balance,
[f_in, "--check"],
)
assert result.exit_code == 1
# blacklisting regions
blacklist = pd.DataFrame(
{
"chrom": ["chr1", "chr2"],
"start": [5, 10],
"end": [10, 20],
},
columns=["chrom", "start", "end"],
)
blacklist.to_csv("blacklist.bed", sep="\t", index=False, header=False)
result = runner.invoke(
balance,
[
f_in,
"--ignore-diags",
"2",
"--mad-max",
"0",
"--min-nnz",
"0",
"--tol",
"0.05",
"--blacklist",
"blacklist.bed",
"--stdout",
],
)
assert result.exit_code == 0
|
