def test_cli_genome_list(tmp_dir, capsys):
config_file = os.path.join(tmp_dir, "test_cli_genome.motifscanrc")
config = Config(config_file)
config.set_genome_path("hg19", "/path/to/genome1")
config.set_genome_path("hg38", "/path/to/genome2")
config.write()
args = parser.parse_args(["genome", "--list"])
run(args=args, config_file=config_file)
captured = capsys.readouterr()
assert captured.out == "hg19\nhg38\n"
def test_cli_genome_uninstall(genome_root, tmp_dir):
config_file = os.path.join(tmp_dir, "test_cli_genome.motifscanrc")
config = Config(config_file)
config.set_genome_dir(tmp_dir)
config.write()
args = parser.parse_args(["genome", "--uninstall", "test_genome"])
run(args=args, config_file=config_file)
config = Config(config_file)
assert not config.has_genome_assembly("test_genome")
genome_path = os.path.join(tmp_dir, "test_genome")
assert not os.path.isdir(genome_path)
args = parser.parse_args(["genome", "--uninstall", "test_genome1"])
with pytest.raises(SystemExit):
run(args=args, config_file=config_file)
def test_cli_genome_install(genome_root, tmp_dir):
config_file = os.path.join(tmp_dir, "test_cli_genome.motifscanrc")
config = Config(config_file)
config.set_genome_dir(tmp_dir)
config.write()
fasta_path = os.path.join(genome_root, "test", "test.fa")
gene_path = os.path.join(genome_root, "test", "test_gene_annotation.txt")
args = parser.parse_args([
"genome", "--install", "-n", "test_genome", "-i", fasta_path, "-a",
gene_path
])
run(args=args, config_file=config_file)
genome_path = os.path.join(tmp_dir, "test_genome")
genome = Genome(name="test_genome", path=genome_path)
assert genome.fetch_sequence("chr1", 0, 10) == "AaTtCcGgNn"
assert genome.genes
config = Config(config_file)
assert config.has_genome_assembly("test_genome")
assert config.get_genome_path("test_genome") == genome_path
def test_cli_genome_search(capsys):
args = parser.parse_args(["genome", "--search", "human"])
run(args=args)
captured = capsys.readouterr()
assert captured.out
def test_cli_genome_list_remote(capsys):
args = parser.parse_args(["genome", "--list-remote"])
run(args=args)
captured = capsys.readouterr()
assert captured.out