if environ.get("TRAVIS"):
max_examples = 100
deadline = None
else:
max_examples = 1000
deadline = None
merge_command = "bedtools merge -o first -c 6 {} -i <(sort -k1,1 -k2,2n {})"
@pytest.mark.bedtools
@pytest.mark.parametrize("strand", [True, False])
@settings(max_examples=max_examples,
deadline=deadline,
suppress_health_check=HealthCheck.all())
@given(gr=dfs_min()) # pylint: disable=no-value-for-parameter
def test_merge(gr, strand):
bedtools_strand = {True: "-s", False: ""}[strand]
print(gr)
with tempfile.TemporaryDirectory() as temp_dir:
f1 = "{}/f1.bed".format(temp_dir)
gr.df.to_csv(f1, sep="\t", header=False, index=False)
cmd = merge_command.format(bedtools_strand, f1)
print(cmd)
# ignoring bandit security warning. All strings created by test suite
result = subprocess.check_output( # nosec
s4vectors_result.runs,
equal_nan=False)
assert np.allclose(result_pyranges.values,
s4vectors_result.values,
equal_nan=True)
rle_commute_how = ["__add__", "__mul__"]
@pytest.mark.parametrize("how", rle_commute_how)
@settings(max_examples=max_examples,
deadline=deadline,
timeout=unlimited,
suppress_health_check=HealthCheck.all())
@given(gr=dfs_min(), gr2=dfs_min())
def test_commutative_rles(gr, gr2, how):
cv = gr.to_rle(strand=True)
cv2 = gr2.to_rle(strand=True)
method = getattr(cv, how)
method2 = getattr(cv2, how)
result = method(cv2)
result2 = method2(cv)
assert result == result2, "\n".join(
[str(e) for e in [cv, cv2, result, result2, "---" * 10]])