def test_run(self):
# taken from MinCED test files
fn = 'Aquifex_aeolicus_VF5.fna'
query = _get_named_data_path(fn)
exp = splitext(query)[0]
params = [{
'-searchWL': '8',
'gff': True,
'gffFull': False,
'spacers': False
}, {
'-searchWL': '8',
'-minNR': '3',
'gffFull': True,
'gff': False,
'spacers': False
}, {
'gff': True,
'spacers': True,
'gffFull': False
}]
exp_fps = ['.gff', '.gffFull', '.gff']
for param, s in zip(params, exp_fps):
res = run(query, self.tmp_dir, **param)
self.assertTrue(cmp(res.params['out'].value, exp + s))
def test_run(self):
# taken from MinCED test files
fn = 'Aquifex_aeolicus_VF5.fna'
query = _get_named_data_path(fn)
exp = splitext(query)[0]
params = [
{'-searchWL': '8', 'gff': True, 'gffFull': False, 'spacers': False},
{'-searchWL': '8', '-minNR': '3', 'gffFull': True, 'gff': False, 'spacers': False},
{'gff': True, 'spacers': True, 'gffFull': False}]
exp_fps = ['.gff', '.gffFull', '.gff']
for param, s in zip(params, exp_fps):
res = run(query, self.tmp_dir, **param)
self.assertTrue(
cmp(res.params['out'].value, exp + s))
def test_run_wrong_input(self):
for fp in self.negative_fps:
# 'empty' file raises JAVA (minced) error
with self.assertRaises(CalledProcessError):
run(fp, self.tmp_dir)
def test_run_wrong_input(self):
for fp in self.negative_fps:
# 'empty' file raises JAVA (minced) error
with self.assertRaises(CalledProcessError):
run(fp, self.tmp_dir)
