def test_default_database_18S(input_dir=os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "example"))):
args = [
"-i", input_dir, "-m", "18S", "-t", "contig", "-f", "SSUF", "-r",
"SSUR", "-o", "test"
]
sys.argv[1:] = args
cryptogenotyper_main()
def test_default_database_gp60_contiginput(input_dir=os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "example"))):
print(os.getcwd(), os.listdir(input_dir))
args = [
"-i", input_dir, "-m", "gp60", "-t", "contig", "-f", "gp60F", "-r",
"gp60R", "-o", "test"
]
sys.argv[1:] = args
cryptogenotyper_main()
def test_default_singlefile(input_dir=os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "example"))):
os.chdir(input_dir)
args = [
"-i", "P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1", "-m", "18S",
"-t", "forward", "-f", "SSUF", "-r", "SSUR", "-o", "test"
]
sys.argv[1:] = args
cryptogenotyper_main()
def test_custom_database_gp60_contiginput(input_dir=os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "example"))):
args = [
"-i", input_dir, "-m", "gp60", "-t", "contig", "-f", "gp60F", "-r",
"gp60R", "-d",
os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "reference_database",
"gp60_ref.fa")), "-o", "test"
]
sys.argv[1:] = args
cryptogenotyper_main()