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import os
import sys
import pytest
# Make sure all tests import pybedtools + genomepy anew
@pytest.fixture(autouse=True)
def cleanup_imports():
yield
del_mods = [mod for mod in sys.modules if "pybedtools" in mod or "genomepy" in mod]
for mod in del_mods:
del sys.modules[mod]
def test_genomepy_not_installed():
import pybedtools
if "genomepy" in sys.modules:
del sys.modules["genomepy"]
genome = "pybedtools/test/data/genome.fa"
d = pybedtools.helpers.get_chromsizes_from_genomepy(genome)
assert d is None
with pytest.raises(OSError):
pybedtools.chromsizes(genome)
with pytest.raises(OSError):
pybedtools.chromsizes("non-existing")
def test_chromsizes_from_genomepy():
import pybedtools
if "genomepy" not in sys.modules:
pytest.skip("genomepy not instlled -- skipping test")
genome = "pybedtools/test/data/genome.fa"
try:
d = pybedtools.helpers.get_chromsizes_from_genomepy(genome)
print(pybedtools.chromsizes(genome))
assert d["chr1"] == (0, 10)
d = pybedtools.chromsizes(genome)
assert d["chr3"] == (0, 30)
finally:
# Make sure all genomepy files get deleted
fnames = [genome + ext for ext in [".fai", ".sizes"]]
fnames.append(genome.replace(".fa", ".gaps.bed"))
for fname in fnames:
if os.path.exists(fname):
os.unlink(fname)
assert None == pybedtools.helpers.get_chromsizes_from_genomepy("non-existing")
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