def test_str_cli_generator():
"""
Tests if str_cli_generator() is working correctlly.
"""
# Define arguments
arg = mockups.Arguments()
k_val = 4
outfile = "str_K4_rep1"
arg.params = None
seed = None
mock_cli = ["EP", "-K", str(k_val), "-i", "IF", "-o", outfile]
returned_cli, returned_outfile = sw.str_cli_generator(arg, k_val, 1, seed)
assert returned_cli == mock_cli
assert returned_outfile == outfile
# Add a seed to the test
seed = "1234"
mock_cli += ["-D", "1234"]
returned_cli, returned_outfile = sw.str_cli_generator(arg, k_val, 1, seed)
assert returned_cli == mock_cli
assert returned_outfile == outfile
# Add an argument to the test
arg.params = "test"
mock_cli += arg.params
returned_cli, returned_outfile = sw.str_cli_generator(arg, k_val, 1, seed)
assert returned_cli == mock_cli
assert returned_outfile == outfile
def test_str_param_checker():
"""
Tests if the STRUCTURE parameter file checker is working.
"""
arg = mockups.Arguments()
arg.infile = "smalldata/Reduced_dataset.structure"
arg.params = "mainparams"
sw.str_param_checker(arg)
assert arg.params == ["-m", "mainparams", "-e", "extraparams"]
def test_vcf_to_matrix():
"""
Tests if vcf_to_matrix() is working correctlly.
Converts a known file, and compares the result with a known good conversion
"""
# Define arguments
arg = mockups.Arguments()
arg.infile = "smalldata/SmallTestData.vcf"
k_val = 4
alsw.vcf_to_matrix(arg.infile)
assert filecmp.cmp(arg.infile[:-4] + ".tsv",
"smalldata/SmallTestData_reference.tsv")
def test_alstr_cli_generator():
"""
Tests if alstr_cli_generator() is working correctlly.
"""
# Define arguments
arg = mockups.Arguments()
arg.infile += ".bed"
k_val = 4
# "Rscript", arg.external_prog, infile, str(k_val), output_file
mock_cli = ["Rscript", "EP", "IF", str(k_val), "alstr_K4"]
returned_cli, out_file = alsw.alstr_cli_generator(arg, k_val)
assert returned_cli == mock_cli
assert out_file == "alstr_K4"
def test_mav_cli_generator():
"""
Tests if mav_cli_generator() is working correctlly.
"""
# Define arguments
arg = mockups.Arguments()
k_val = 4
parameters = {}
mock_cli = ["EP", "-Kmin", str(k_val), "-Kmax", str(k_val), "-data",
"IF", "-outputRoot", "mav_K4/", "-masterRoot", "/",
"-parameters", "smalldata/parameters.txt"]
# Perform test with and without TI
for ti_value in (False, True):
arg.notests = ti_value
if arg.notests is True:
mock_cli += ["-thermodynamic_on", "f"]
returned_cli, out_dir = mw.mav_cli_generator(arg, k_val, parameters)
assert returned_cli == mock_cli
assert out_dir == "mav_K4/"
def test_fs_cli_generator():
"""
Tests if fs_cli_generator() is working correctlly.
"""
# Define arguments
arg = mockups.Arguments()
k_val = 4
for prog in ["EP", "EP.py"]:
arg.external_prog = prog
mock_cli = [
prog, "-K",
str(k_val), "--input", "IF", "--output", "fS_run_K", "--format",
"str", "--prior=logistic"
]
if prog.endswith(".py"):
mock_cli = ["python2"] + mock_cli
returned_cli, returned_outdir = fsw.fs_cli_generator(k_val, arg)
assert returned_cli == mock_cli
assert returned_outdir == "fS_run_K"