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"])