def test_alignment_to_clustal_with_bad_input(self): BAD = StringIO('\n'.join(['dshfjsdfhdfsj', 'hfsdjksdfhjsdf'])) result = _clustal_to_alignment(BAD, strict=False) self.assertEqual(dict(result), {}) # should fail unless we turned strict processing off with self.assertRaises(ClustalFormatError): BAD.seek(0) dict(_clustal_to_alignment(BAD))
def test_valid_alignment_to_clustal_and_clustal_to_alignment(self): import os for valid_out in self.valid_clustal_out: fname = "test.aln" testfile = open(fname, 'w') result_before = _clustal_to_alignment(valid_out) _alignment_to_clustal(result_before, testfile) testfile.close() testfile = open(fname, 'r') result_after = _clustal_to_alignment(testfile) self.assertEquals(result_before, result_after) os.remove(fname)
def test_invalid_alignment_to_clustal_and_clustal_to_alignment(self): for invalid_out in self.invalid_clustal_out: with self.assertRaises(ClustalFormatError): dict(_clustal_to_alignment(invalid_out, strict=True))
def test_alignment_to_clustal_with_empty_input(self): result = _clustal_to_alignment(StringIO()) self.assertEqual(dict(result), {})