def test_read_mash_dist():
mash.dist('tests/dummy_fastq/*fastq',
output_file='tests/distances.tab',
returncmd=True)
results = mash.read_mash_output('tests/distances.tab')
assert results[1].reference == 'tests/dummy_fastq/single.fastq' \
and results[1].query == 'tests/dummy_fastq/test_R2.fastq' \
and results[1].distance == 0.00763536
os.remove('tests/distances.tab')
def test_mash_dist_call_multithreaded():
out, err, cmd = mash.dist('tests/dummy_fastq/*fastq',
output_file='tests/distances.tab',
returncmd=True,
threads=4)
assert cmd == 'mash dist tests/dummy_fastq/*fastq -p 4 > tests/distances.tab'
os.remove('tests/distances.tab')
def test_mash_dist_call_kwargs():
out, err, cmd = mash.dist('tests/dummy_fastq/*fastq',
output_file='tests/distances.tab',
returncmd=True,
s='34')
assert cmd == 'mash dist tests/dummy_fastq/*fastq -p 1 -s 34 > tests/distances.tab'
os.remove('tests/distances.tab')
def test_dist_no_input_files():
with pytest.raises(ValueError):
mash.dist()