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",
)
