biopython/Tests/test_KeyWList.py

# Copyright 1999 by Jeffrey Chang.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for KeyWList."""

import os.path
import unittest

from Bio.SwissProt import KeyWList


class KeyWListTest(unittest.TestCase):
    """Tests for KeyWList."""

    def test_parse(self):
        """Test parsing keywlist.txt works."""
        filename = os.path.join("SwissProt", "keywlist.txt")
        with open(filename) as handle:
            records = KeyWList.parse(handle)

            # Testing the first record
            record = next(records)
            self.assertEqual(record["ID"], "2Fe-2S.")
            self.assertEqual(record["AC"], "KW-0001")
            self.assertEqual(
                record["DE"],
                "Protein which contains at least one 2Fe-2S iron-sulfur cluster: 2 iron atoms complexed to 2 inorganic sulfides and 4 sulfur atoms of cysteines from the protein.",
            )
            self.assertEqual(
                record["SY"],
                "Fe2S2; [2Fe-2S] cluster; [Fe2S2] cluster; Fe2/S2 (inorganic) cluster; Di-mu-sulfido-diiron; 2 iron, 2 sulfur cluster binding.",
            )
            self.assertEqual(len(record["GO"]), 1)
            self.assertEqual(
                record["GO"], ["GO:0051537; 2 iron, 2 sulfur cluster binding"]
            )
            self.assertEqual(len(record["HI"]), 2)
            self.assertEqual(record["HI"][0], "Ligand: Iron; Iron-sulfur; 2Fe-2S.")
            self.assertEqual(record["HI"][1], "Ligand: Metal-binding; 2Fe-2S.")
            self.assertEqual(record["CA"], "Ligand.")

            # Testing the second record
            record = next(records)
            self.assertEqual(record["IC"], "Molecular function.")
            self.assertEqual(record["AC"], "KW-9992")
            self.assertEqual(
                record["DE"],
                "Keywords assigned to proteins due to their particular molecular function.",
            )

            # Testing the third record
            record = next(records)
            self.assertEqual(record["ID"], "Zymogen.")
            self.assertEqual(record["AC"], "KW-0865")
            self.assertEqual(
                record["DE"],
                "The enzymatically inactive precursor of mostly proteolytic enzymes.",
            )
            self.assertEqual(record["SY"], "Proenzyme.")
            self.assertEqual(len(record["HI"]), 1)
            self.assertEqual(record["HI"][0], "PTM: Zymogen.")
            self.assertEqual(record["CA"], "PTM.")

    def test_parse2(self):
        """Parsing keywlist2.txt (without header and footer)."""
        filename = os.path.join("SwissProt", "keywlist2.txt")
        with open(filename) as handle:
            records = KeyWList.parse(handle)

            # Testing the first record
            record = next(records)
            self.assertEqual(record["ID"], "2Fe-2S.")
            self.assertEqual(record["AC"], "KW-0001")
            self.assertEqual(
                record["DE"],
                "Protein which contains at least one 2Fe-2S iron-sulfur cluster: 2 iron atoms complexed to 2 inorganic sulfides and 4 sulfur atoms of cysteines from the protein.",
            )
            self.assertEqual(
                record["SY"],
                "Fe2S2; [2Fe-2S] cluster; [Fe2S2] cluster; Fe2/S2 (inorganic) cluster; Di-mu-sulfido-diiron; 2 iron, 2 sulfur cluster binding.",
            )
            self.assertEqual(len(record["GO"]), 1)
            self.assertEqual(
                record["GO"], ["GO:0051537; 2 iron, 2 sulfur cluster binding"]
            )
            self.assertEqual(len(record["HI"]), 2)
            self.assertEqual(record["HI"][0], "Ligand: Iron; Iron-sulfur; 2Fe-2S.")
            self.assertEqual(record["HI"][1], "Ligand: Metal-binding; 2Fe-2S.")
            self.assertEqual(record["CA"], "Ligand.")

            # Testing the second record
            record = next(records)
            self.assertEqual(record["ID"], "3D-structure.")
            self.assertEqual(record["AC"], "KW-0002")
            self.assertEqual(
                record["DE"],
                "Protein, or part of a protein, whose three-dimensional structure has been resolved experimentally (for example by X-ray crystallography or NMR spectroscopy) and whose coordinates are available in the PDB database. Can also be used for theoretical models.",
            )
            self.assertEqual(len(record["HI"]), 1)
            self.assertEqual(record["HI"][0], "Technical term: 3D-structure.")
            self.assertEqual(record["CA"], "Technical term.")

            # Testing the third record
            record = next(records)
            self.assertEqual(record["ID"], "3Fe-4S.")
            self.assertEqual(record["AC"], "KW-0003")
            self.assertEqual(
                record["DE"],
                "Protein which contains at least one 3Fe-4S iron-sulfur cluster: 3 iron atoms complexed to 4 inorganic sulfides and 3 sulfur atoms of cysteines from the protein. In a number of iron-sulfur proteins, the 4Fe-4S cluster can be reversibly converted by oxidation and loss of one iron ion to a 3Fe-4S cluster.",
            )
            self.assertEqual(record["SY"], "")
            self.assertEqual(len(record["GO"]), 1)
            self.assertEqual(
                record["GO"], ["GO:0051538; 3 iron, 4 sulfur cluster binding"]
            )
            self.assertEqual(len(record["HI"]), 2)
            self.assertEqual(record["HI"][0], "Ligand: Iron; Iron-sulfur; 3Fe-4S.")
            self.assertEqual(record["HI"][1], "Ligand: Metal-binding; 3Fe-4S.")
            self.assertEqual(record["CA"], "Ligand.")


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)