def test_filename_basename_keep_filtered_gc_bounds_min_length(self):
for min_length in self.min_length_test_set:
test_args = [
("fastq_filtrator.py", "--min_length", min_length,
"--gc_bounds", "20", "21", "--keep_filtered",
"--output_base_name", "filtered", "example.fastq"),
("fastq_filtrator.py", "example.fastq", "--min_length",
min_length, "--gc_bounds", "20", "21", "--keep_filtered",
"--output_base_name", "filtered"),
("fastq_filtrator.py", "--output_base_name", "filtered",
"--min_length", min_length, "example.fastq", "--gc_bounds",
"20", "21", "--keep_filtered"),
("fastq_filtrator.py", "--output_base_name", "filtered",
"--keep_filtered", "--min_length", min_length, "--gc_bounds",
"20", "21", "example.fastq"),
("fastq_filtrator.py", "--output_base_name", "filtered",
"--keep_filtered", "--gc_bounds", "20", "21", "--min_length",
min_length, "example.fastq")
]
answ = deepcopy(self.output_dict_default)
answ.update(
dict(file_name="example.fastq",
output_base_name="filtered",
keep_filtered=True,
gc_bounds=[20, 21],
min_length=int(min_length)))
for arg_set in test_args:
result = parse_arguments(arg_set)
self.assertDictEqual(result, answ)
def test_filename_basename_keep_filtered_gc_bounds(self):
for gc_bounds in self.gc_bounds_test_set:
test_args = [
("fastq_filtrator.py", "--gc_bounds", *gc_bounds,
"--keep_filtered", "--output_base_name", "filtered",
"example.fastq"),
("fastq_filtrator.py", "example.fastq", "--gc_bounds",
*gc_bounds, "--keep_filtered", "--output_base_name",
"filtered"),
("fastq_filtrator.py", "--output_base_name", "filtered",
"example.fastq", "--gc_bounds", *gc_bounds,
"--keep_filtered"),
("fastq_filtrator.py", "--output_base_name", "filtered",
"--keep_filtered", "--gc_bounds", *gc_bounds, "example.fastq")
]
answ = deepcopy(self.output_dict_default)
if len(gc_bounds) == 2:
answ.update(
dict(file_name="example.fastq",
output_base_name="filtered",
keep_filtered=True,
gc_bounds=[int(gc_bounds[0]),
int(gc_bounds[1])]))
elif len(gc_bounds) == 1:
answ.update(
dict(file_name="example.fastq",
output_base_name="filtered",
keep_filtered=True,
gc_bounds=[int(gc_bounds[0]), 100]))
for arg_set in test_args:
result = parse_arguments(arg_set)
self.assertDictEqual(result, answ)
def test_filename_only(self):
test_args = ["fastq_filtrator.py", "example.fastq"]
answ = deepcopy(self.output_dict_default)
answ.update(dict(file_name="example.fastq",
output_base_name="example"))
result = parse_arguments(test_args)
self.assertDictEqual(result, answ)
def test_filename_and_basename(self):
for base_name in self.base_names_test_set:
test_args = [("fastq_filtrator.py", "--output_base_name",
base_name, "example.fastq"),
("fastq_filtrator.py", "example.fastq",
"--output_base_name", base_name)]
answ = deepcopy(self.output_dict_default)
answ.update(
dict(file_name="example.fastq", output_base_name=base_name))
for arg_set in test_args:
result = parse_arguments(arg_set)
self.assertDictEqual(result, answ)
def test_filename_basename_keep_filtered(self):
test_args = [("fastq_filtrator.py", "--keep_filtered",
"--output_base_name", "filtered", "example.fastq"),
("fastq_filtrator.py", "example.fastq", "--keep_filtered",
"--output_base_name", "filtered"),
("fastq_filtrator.py", "example.fastq",
"--output_base_name", "filtered", "--keep_filtered")]
answ = deepcopy(self.output_dict_default)
answ.update(
dict(file_name="example.fastq",
output_base_name="filtered",
keep_filtered=True))
for arg_set in test_args:
result = parse_arguments(arg_set)
self.assertDictEqual(result, answ)