def test_RunGenovo_set_cutoff(self):
"""
Note: There are different type of Errors
Feel free to change/swap/move between ValueError and TypeError
"""
infile_var = "test_infile.fasta"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir, no_iter=3,
thresh=250, check_exist=False)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, 1.1)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, -1)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, -2.5)
self.assertRaises(ValueError, genovo.set_finalize_cutoff, "string")
try:
genovo.set_finalize_cutoff("3")
except ValueError as e:
self.fail(e)
def test_RunGenovo_simple_finalise(self):
infile_var = "test_infile.fasta"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir, no_iter=3,
thresh=250, check_exist=False)
self.assertEqual(3, len(genovo.finalize._switch))
expected = ["250", self.data_dir + "test_infile.genovo",
self.data_dir + infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
genovo.set_finalize_cutoff(300)
expected = ["300", self.data_dir + "test_infile.genovo",
self.data_dir + infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)
infile_var = "VICTORY!!!.fasta"
genovo.set_infile_name(infile_var)
expected = ["300", self.data_dir + "test_infile.genovo",
infile_var + ".dump.best"]
self.assertEqual(genovo.finalize.get_all_switches(), expected)