def test_format_function_arguments(self): app = MothurClassifySeqs({ 'reference': '/home/myuser/ref-seqs.fasta', 'taxonomy': '/home/MyUser/data/tax.txt', 'cutoff': 80, }) obs_args = app._format_function_arguments( ['reference', 'taxonomy', 'cutoff', 'iters']) exp_args = ( "reference=/home/myuser/ref\\-seqs.fasta, " "taxonomy=/home/MyUser/data/tax.txt, cutoff=80") self.assertEqual(obs_args, exp_args)
def test_compile_mothur_script(self): app = MothurClassifySeqs({ 'reference': '/home/myuser/ref-seqs.fasta', 'taxonomy': '/home/MyUser/data/tax.txt', 'cutoff': 80, }) app._input_filename = "/my/input.fasta" exp_script = ( "#classify.seqs(fasta=/my/input.fasta, " "reference=/home/myuser/ref\-seqs.fasta, " "taxonomy=/home/MyUser/data/tax.txt, " "cutoff=80)") self.assertEqual(app._compile_mothur_script(), exp_script)