def test_process_args_expected_keywords(self, args):
res = process_args(args)
expected_keys = [
"fasta_file_list", "hmms_file_list", "evalue", "percent_bitscore",
"output_dir", "cpu"
]
assert sorted(res.keys()) == sorted(expected_keys)
def test_process_args_custom_output(self, args):
args.output_dir = "custom_out"
res = process_args(args)
assert res["output_dir"] == "custom_out"
def test_process_args_custom_cpu(self, args):
args.cpu = 4
res = process_args(args)
assert res["cpu"] == 4
def test_process_args_custom_bitscore(self, args):
args.bitscore = 0.5
res = process_args(args)
assert res["percent_bitscore"] == 0.5
def test_process_args_default_bitscore(self, args):
args.bitscore = None
res = process_args(args)
assert res["percent_bitscore"] == 0.85
def test_process_args_custom_evalue(self, args):
args.evalue = 1e-5
res = process_args(args)
assert res["evalue"] == 0.00001
def test_process_args_default_evalue(self, args):
args.evalue = None
res = process_args(args)
assert res["evalue"] == 0.001
def test_process_args_hmm_file_dne(self, args):
args.hmm = "some/file/that/doesnt/exist"
with pytest.raises(SystemExit):
process_args(args)