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"""
Useful things for debugging CLI failures:
pytest --pdb
print(result.output)
import traceback; traceback.print_tb(result.exception.__traceback__)
"""
import os
import os.path as op
import click
import pytest
from click.testing import CliRunner
from cooler.cli import _util as util
from cooler.cli import cli
from cooler.util import cmd_exists
testdir = op.realpath(op.dirname(__file__))
datadir = op.join(testdir, "data")
def test_cli():
runner = CliRunner()
result = runner.invoke(cli, ["-h"])
assert result.exit_code == 0
result = runner.invoke(cli, ["-V"])
assert result.exit_code == 0
def test_verbose():
runner = CliRunner()
result = runner.invoke(cli, ["info", op.join(datadir, "toy.symm.upper.2.cool")])
assert result.exit_code == 0
result = runner.invoke(
cli, ["-v", "info", op.join(datadir, "toy.symm.upper.2.cool")]
)
assert result.exit_code == 0
pytest.importorskip("psutil")
result = runner.invoke(
cli, ["-vv", "info", op.join(datadir, "toy.symm.upper.2.cool")]
)
assert result.exit_code == 0
### HELPERS ###
def test_makebins():
runner = CliRunner()
result = runner.invoke(cli, ["makebins", op.join(datadir, "toy.chrom.sizes"), "8"])
assert result.exit_code == 0
assert (
result.output
== "chr1\t0\t8\nchr1\t8\t16\nchr1\t16\t24\nchr1\t24\t32\nchr2\t0\t8\nchr2\t8\t16\nchr2\t16\t24\nchr2\t24\t32\n" # noqa
)
result = runner.invoke(
cli,
[
"makebins",
"--header",
"--rel-ids",
"1",
op.join(datadir, "toy.chrom.sizes"),
"8",
],
)
assert result.exit_code == 0
assert (
result.output
== "chrom\tstart\tend\tid\nchr1\t0\t8\t1\nchr1\t8\t16\t2\nchr1\t16\t24\t3\nchr1\t24\t32\t4\nchr2\t0\t8\t1\nchr2\t8\t16\t2\nchr2\t16\t24\t3\nchr2\t24\t32\t4\n" # noqa
)
@pytest.mark.skipif(
os.name == "nt",
reason="Non-reproducible off-by-one bug on Win32 GitHub runner"
)
def test_digest():
runner = CliRunner()
result = runner.invoke(
cli,
[
"digest",
op.join(datadir, "toy.chrom.sizes"),
op.join(datadir, "toy.fasta"),
"HindIII",
],
)
assert result.exit_code == 0
assert result.output == "chr1\t0\t32\nchr2\t0\t32\n"
result = runner.invoke(
cli,
[
"digest",
"--header",
"--rel-ids",
"1",
op.join(datadir, "toy.chrom.sizes"),
op.join(datadir, "toy.fasta"),
"HindIII",
],
)
assert result.exit_code == 0
assert result.output == "chrom\tstart\tend\tid\nchr1\t0\t32\t1\nchr2\t0\t32\t1\n"
@pytest.mark.skipif(
not cmd_exists("bgzip") or not cmd_exists("pairix"),
reason="missing command line requirements for csort",
)
def test_csort():
runner = CliRunner()
with runner.isolated_filesystem():
result = runner.invoke(
cli,
[
"csort",
"-c1",
"2",
"-p1",
"3",
"-c2",
"4",
"-p2",
"5",
"-p",
1,
op.join(datadir, "toy.pairs"),
op.join(datadir, "toy.chrom.sizes"),
"-o",
"test.pairs.blksrt",
],
)
assert result.exit_code == 0
def test_util_delimited_tuple():
param = util.DelimitedTuple(sep=",")
result = param.convert("spam,eggs", None, None)
assert result == ("spam", "eggs")
param = util.DelimitedTuple(sep=",", type=int)
result = param.convert("10,20", None, None)
assert result == (10, 20)
with pytest.raises(click.BadParameter):
param.convert("spam,20", None, None)
def test_util_parse_kv_list_param():
result = util.parse_kv_list_param("spam=1,eggs=2,apples=oranges,x=[0,0,0]")
assert result == {
"spam": 1,
"eggs": 2,
"apples": "oranges",
"x": [0, 0, 0],
}
def test_util_parse_field_param():
util.parse_field_param("count=7:dtype=int,agg=sum")
util.parse_field_param("count:dtype=int,agg=sum", includes_colnum=False)
util.parse_field_param("count:dtype=int", includes_agg=False)
def test_parse_bins():
cs1, bins1 = util.parse_bins(op.join(datadir, "toy.chrom.sizes") + ":8")
cs2, bins2 = util.parse_bins(op.join(datadir, "toy.bins.8.bed"))
assert cs1.equals(cs2)
assert (bins1 == bins2).all().all()
def test_check_ncpus():
assert util.check_ncpus(10) <= 10
|
