def test_toPhylip(self):
"""Alignment should return PHYLIP string format correctly"""
align_norm = Alignment( ['ACDEFGHIKLMNPQRSTUVWY-',
'ACDEFGHIKLMNPQRSUUVWF-',
'ACDEFGHIKLMNPERSKUVWC-',
'ACNEFGHIKLMNPQRS-UVWP-',
])
phylip_str, id_map = align_norm.toPhylip()
self.assertEqual(phylip_str, """4 22\nseq0000001 ACDEFGHIKLMNPQRSTUVWY-\nseq0000002 ACDEFGHIKLMNPQRSUUVWF-\nseq0000003 ACDEFGHIKLMNPERSKUVWC-\nseq0000004 ACNEFGHIKLMNPQRS-UVWP-""")
self.assertEqual(id_map, {'seq0000004': 3, 'seq0000001': 0, 'seq0000003': 2, 'seq0000002': 1})
align_rag = Alignment( ['ACDEFGHIKLMNPQRSTUVWY-',
'ACDEFGHIKLMNPQRSUUVWF-',
'ACDEFGHIKLMNPERSKUVWC-',
'ACNEFGHIKLMNUVWP-',
])
self.assertRaises(ValueError, align_rag.toPhylip)
