def test_RunGenovo_set_number_of_iter(self):
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_assemble_number_of_iter, 1.1)
self.assertRaises(ValueError, genovo.set_assemble_number_of_iter, -1)
self.assertRaises(ValueError, genovo.set_assemble_number_of_iter, "string")
self.assertRaises(ValueError, genovo.set_assemble_number_of_iter, "5.9")
try:
genovo.set_assemble_number_of_iter("300")
except ValueError as e:
self.fail(e)
self.assertEqual(genovo.assemble.get_all_switches()[run_genovo.ASSEMBLE_NO_ITER_POSITION - 1], "300")
def test_RunGenovo_simple_assemble(self):
infile_var = "all_read.fa"
genovo = RunGenovo(infile=infile_var, pdir=self.data_dir,
wdir=self.working_dir, no_iter=3, thresh=250,
check_exist=False)
expected = [self.working_dir + infile_var, "3"]
self.assertEqual(genovo.assemble.get_all_switches(), expected)
genovo.set_assemble_number_of_iter(10)
expected = [self.working_dir + infile_var, "10"]
self.assertEqual(genovo.assemble.get_all_switches(), expected)
infile_var = "test_infile.fasta"
genovo.set_infile_name(infile_var)
self.assertEqual(genovo.assemble.get_all_switches(), [infile_var, "10"])
