def test_name_string():
'''
assert true when the input is a string > len 0
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
assert detect_obj._name_exists('somestring')
def test_four_isolates():
'''
confirm that min of 4 rows are present
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
tab = pandas.DataFrame({'A': [1, 2, 3, 4]})
assert detect_obj.min_four_samples(tab) == False
def test_notfour_isolates():
'''
return false when less than 4 rows are present
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
tab = pandas.DataFrame({'A': [1, 2, 3]})
assert detect_obj.min_four_samples(tab)
def test_3col_dimensions():
'''
return True when correct number of columns
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
tab = pandas.DataFrame({'A': [1], 'B': [2], 'C': [3]})
assert detect_obj.three_cols(tab)
def test_2col_dimensions():
'''
return False when wrong number of columns present
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
tab = pandas.DataFrame({'A': [1], 'B': [2]})
assert detect_obj.three_cols(tab) == False
def test_name_non_string():
'''
if a non string input is used return false
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
with pytest.raises(SystemExit):
detect_obj._name_exists(9)
def test_name_empty_string():
'''
confirm that False is returned if a 0 length strin is input
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
with pytest.raises(SystemExit):
detect_obj._name_exists('')
def test_path_exists():
'''
test that path_exists returns True
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
p = pathlib.Path('bohra', 'tests', 'test_file.txt')
detect_obj = RunSnpDetection()
assert detect_obj.path_exists(p)
def test_with_missing():
'''
return False if missing data present
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
tab = pandas.DataFrame({'A':[1,2,4, numpy.nan], 'B':[5,6,7,8], 'C':[9,10,11,12]})
assert detect_obj.all_data_filled(tab) == False
def test_missing():
'''
a full dataframe returns true
'''
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
tab = pandas.DataFrame({'A':[1,2,3,4], 'B':[5,6,7,8], 'C':[9,10,11,12]})
assert detect_obj.all_data_filled(tab)
def test_structure():
with patch.object(RunSnpDetection, "__init__", lambda x: None):
detect_obj = RunSnpDetection()
tab = pandas.DataFrame({
'A': [1, 2, 3, 4],
'B': [5, 6, 7, 8],
'C': [9, 10, 11, 12]
})
assert detect_obj.check_input_structure(tab) == True
def run_pipeline(args):
'''
Run the pipeline for the first time
'''
R = RunSnpDetection(args)
return (R.run_pipeline())
