def test_parse_swissprot(self): with open(self.report_path_generic_bank, "r") as report: ids, errors = parseSummary(report) self.assertEqual(ids, self.ids) self.assertEqual(errors, []) with open(self.report_path_generic_bank, "r") as report: ids, errors = parseSummary(report, From=5) self.assertEqual(ids, self.ids[4:]) self.assertEqual(errors, []) with open(self.report_path_generic_bank, "r") as report: ids, errors = parseSummary(report, To=10) self.assertEqual(ids, self.ids[:10]) self.assertEqual(errors, []) with open(self.report_path_generic_bank, "r") as report: ids, errors = parseSummary(report, From=10, To=15) self.assertEqual(ids, self.ids[9:15]) self.assertEqual(errors, [])
def test_parse_pdb(self): with open(self.report_path_pdb, "r") as report: ids, errors = parseSummary(report) report_ids = [ Entry("pdb", "4f4c"), Entry("pdb", "4lsg"), Entry("pdb", "4lsg"), Entry("pdb", "4ksd"), Entry("pdb", "4ksc"), ] self.assertEqual(ids[0:5], report_ids) self.assertEqual(errors, [])
def test_parse_pdb_bad_header(self): with open(self.report_path_bad_header, "r") as report: ids, errors = parseSummary(report) self.assertListEqual(ids, []) self.assertEqual(len(errors), 313) self.assertEqual( errors[0], "ERROR cannot parse hit 9450_pdb mol:protein length:451 Succinoglycan biosynthesis protein 77 1e-14 : skip this Hit", ) self.assertEqual( errors[-1], "ERROR cannot parse hit 16678_pdb mol:protein length:727 AMINE OXIDASE 42 0.005 : skip this Hit", )