def test_cli_config_set_default_motif(tmp_dir):
args = parser.parse_args(
["config", "--set-default-motif", "/path/to/motif/root"])
config_file = os.path.join(tmp_dir, "test_cli_config.motifscanrc")
run(args=args, config_file=config_file)
config = Config(config_file)
assert config.get_motif_dir() == "/path/to/motif/root"
def test_cli_config_set_motif(tmp_dir):
args = parser.parse_args(
["config", "--set-motif", "motif_set", "/path/to/motif"])
config_file = os.path.join(tmp_dir, 'test_cli_config.motifscanrc')
run(args=args, config_file=config_file)
config = Config(config_file)
assert config.has_motif_set("motif_set")
assert config.get_motif_path("motif_set") == "/path/to/motif"
def test_cli_config_set_genome(tmp_dir):
args = parser.parse_args(
["config", "--set-genome", "hg19", "/path/to/genome"])
config_file = os.path.join(tmp_dir, 'test_cli_config.motifscanrc')
run(args=args, config_file=config_file)
config = Config(config_file)
assert config.has_genome_assembly("hg19")
assert config.get_genome_path("hg19") == "/path/to/genome"
def test_cli_config_get_genome(tmp_dir, capsys):
config_file = os.path.join(tmp_dir, "test_cli_config.motifscanrc")
config = Config(config_file)
config.set_genome_path("hg19", "/path/to/genome")
config.write()
args = parser.parse_args(["config", "--get-genome", "hg19"])
run(args=args, config_file=config_file)
captured = capsys.readouterr()
assert captured.out == "/path/to/genome\n"
with pytest.raises(SystemExit):
args = parser.parse_args(["config", "--get-genome", "hg38"])
run(args=args, config_file=config_file)
def test_cli_config_get_motif(tmp_dir, capsys):
config_file = os.path.join(tmp_dir, "test_cli_config.motifscanrc")
config = Config(config_file)
config.set_motif_path("motif_set", "/path/to/motif")
config.write()
args = parser.parse_args(["config", "--get-motif", "motif_set"])
run(args=args, config_file=config_file)
captured = capsys.readouterr()
assert captured.out == "/path/to/motif\n"
with pytest.raises(SystemExit):
args = parser.parse_args(["config", "--get-motif", "motif_set1"])
run(args=args, config_file=config_file)
def test_cli_config_rm_genome(tmp_dir):
config_file = os.path.join(tmp_dir, "test_cli_config.motifscanrc")
config = Config(config_file)
config.set_genome_path("hg19", "/path/to/genome")
config.write()
args = parser.parse_args(["config", "--rm-genome", "hg19"])
run(args=args, config_file=config_file)
config = Config(config_file)
assert not config.has_genome_assembly("hg19")
with pytest.raises(GenomeNotFoundError):
config.get_genome_path("hg19")
with pytest.raises(SystemExit):
run(args=args, config_file=config_file)
def test_cli_config_rm_motif(tmp_dir):
config_file = os.path.join(tmp_dir, "test_cli_config.motifscanrc")
config = Config(config_file)
config.set_motif_path("motif_set", "/path/to/motif")
config.write()
args = parser.parse_args(["config", "--rm-motif", "motif_set"])
run(args=args, config_file=config_file)
config = Config(config_file)
assert not config.has_motif_set("motif_set")
with pytest.raises(MotifSetNotFoundError):
config.get_motif_path("motif_set")
with pytest.raises(SystemExit):
run(args=args, config_file=config_file)
def test_cli_config_show(tmp_dir, capsys):
config_file = os.path.join(tmp_dir, "test_cli_config.motifscanrc")
config = Config(config_file)
config.set_genome_dir("/path/to/genome/root")
config.set_motif_dir("/path/to/motif/root")
config.set_genome_path("hg19", "/path/to/genome")
config.set_motif_path("motif_set", "/path/to/motif")
config.write()
args = parser.parse_args(["config", "--show"])
run(args=args, config_file=config_file)
captured = capsys.readouterr()
assert captured.out == "[motifscan]\n" \
"genome_dir: /path/to/genome/root\n" \
"motif_dir: /path/to/motif/root\n\n" \
"[genome]\n" \
"hg19: /path/to/genome\n\n" \
"[motif]\n" \
"motif_set: /path/to/motif\n"