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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
208 lines
8.0 KiB
Python
208 lines
8.0 KiB
Python
# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
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# Revisions copyright 2007 by Michiel de Hoon. All rights reserved.
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# Revisions copyright 2017 by Peter Cock. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests the basic functionality of the KEGG parsers."""
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import unittest
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from Bio.KEGG import Compound
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from Bio.KEGG import Enzyme
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from Bio.KEGG import Map
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from Bio.Pathway import System
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class EnzymeTests(unittest.TestCase):
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"""Tests for Bio.KEGG.Enzyme."""
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def test_sample(self):
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"""enzyme.sample tests."""
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with open("KEGG/enzyme.sample") as handle:
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records = list(Enzyme.parse(handle))
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self.assertEqual(len(records), 8)
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self.assertEqual(records[0].entry, "1.1.1.1")
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self.assertEqual(
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records[0].name,
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[
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"alcohol dehydrogenase",
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"aldehyde reductase",
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"ADH",
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"alcohol dehydrogenase (NAD)",
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"aliphatic alcohol dehydrogenase",
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"ethanol dehydrogenase",
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"NAD-dependent alcohol dehydrogenase",
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"NAD-specific aromatic alcohol dehydrogenase",
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"NADH-alcohol dehydrogenase",
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"NADH-aldehyde dehydrogenase",
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"primary alcohol dehydrogenase",
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"yeast alcohol dehydrogenase",
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],
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)
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self.assertEqual(
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records[0].pathway,
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[
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("PATH", "ec00010", "Glycolysis / Gluconeogenesis"),
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("PATH", "ec00071", "Fatty acid degradation"),
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("PATH", "ec00260", "Glycine, serine and threonine metabolism"),
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("PATH", "ec00350", "Tyrosine metabolism"),
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("PATH", "ec00592", "alpha-Linolenic acid metabolism"),
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("PATH", "ec00625", "Chloroalkane and chloroalkene degradation"),
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("PATH", "ec00626", "Naphthalene degradation"),
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("PATH", "ec00830", "Retinol metabolism"),
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("PATH", "ec00980", "Metabolism of xenobiotics by cytochrome P450"),
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("PATH", "ec00982", "Drug metabolism - cytochrome P450"),
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("PATH", "ec01100", "Metabolic pathways"),
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("PATH", "ec01110", "Biosynthesis of secondary metabolites"),
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("PATH", "ec01120", "Microbial metabolism in diverse environments"),
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("PATH", "ec01130", "Biosynthesis of antibiotics"),
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],
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)
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self.assertEqual(
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records[0].dblinks,
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[
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("ExplorEnz - The Enzyme Database", ["1.1.1.1"]),
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("IUBMB Enzyme Nomenclature", ["1.1.1.1"]),
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("ExPASy - ENZYME nomenclature database", ["1.1.1.1"]),
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("UM-BBD (Biocatalysis/Biodegradation Database)", ["1.1.1.1"]),
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("BRENDA, the Enzyme Database", ["1.1.1.1"]),
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("CAS", ["9031-72-5"]),
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],
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)
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self.assertEqual(records[-1].entry, "2.7.2.1")
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self.assertEqual(
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str(records[-1]).replace(" ", "").split("\n")[:10],
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[
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"ENTRYEC2.7.2.1",
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"NAMEacetatekinase",
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"acetokinase",
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"AckA",
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"AK",
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"acetickinase",
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"acetatekinase(phosphorylating)",
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"CLASSTransferases;",
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"Transferringphosphorus-containinggroups;",
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"Phosphotransferaseswithacarboxygroupasacceptor",
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],
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)
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def test_irregular(self):
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"""enzyme.irregular tests."""
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with open("KEGG/enzyme.irregular") as handle:
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records = list(Enzyme.parse(handle))
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self.assertEqual(len(records), 2)
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self.assertEqual(records[0].entry, "1.14.18.1")
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self.assertEqual(records[-1].entry, "3.4.21.50")
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def test_new(self):
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"""enzyme.new tests."""
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with open("KEGG/enzyme.new") as handle:
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records = list(Enzyme.parse(handle))
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self.assertEqual(len(records), 1)
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self.assertEqual(records[0].entry, "6.2.1.25")
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def test_4letter(self):
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"""enzyme.4letter tests."""
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with open("KEGG/enzyme.4letter") as handle:
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records = list(Enzyme.parse(handle))
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self.assertEqual(len(records), 1)
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self.assertEqual(records[0].entry, "5.4.2.2")
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self.assertEqual(records[0].genes[0], ("HSA", ["5236", "55276"]))
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self.assertEqual(records[0].genes[8], ("CSAB", ["103224690", "103246223"]))
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def test_exceptions(self):
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"""enzyme.exceptions tests."""
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with open("KEGG/enzyme.sample") as handle:
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with self.assertRaises(ValueError) as context:
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list(Enzyme.read(handle))
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self.assertIn(
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"More than one record found in handle", str(context.exception)
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)
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records = Enzyme.parse(handle)
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for i in range(6):
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next(records)
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self.assertRaises(StopIteration, next, records)
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class CompoundTests(unittest.TestCase):
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"""Bio.KEGG.Compound tests."""
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def test_sample(self):
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"""compound.sample tests."""
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with open("KEGG/compound.sample") as handle:
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records = list(Compound.parse(handle))
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self.assertEqual(len(records), 8)
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self.assertEqual(records[1].entry, "C00017")
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self.assertEqual(records[1].mass, "")
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self.assertEqual(records[1].formula, "C2H4NO2R(C2H2NOR)n")
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self.assertEqual(records[1].name, ["Protein"])
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self.assertEqual(
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records[1].pathway, [("PATH", "map00450", "Selenocompound metabolism")]
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)
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self.assertEqual(len(records[1].enzyme), 21)
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self.assertEqual(records[1].enzyme[0], ("2.3.2.6"))
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self.assertEqual(records[1].structures, [])
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self.assertEqual(records[1].dblinks[0], ("PubChem", ["3319"]))
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self.assertEqual(
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str(records[-1]).replace(" ", "").split("\n")[:11],
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[
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"ENTRYC01386",
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"NAMENH2Mec",
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"7-Amino-4-methylcoumarin",
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"FORMULAC10H9NO2",
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"MASS175.0633",
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"DBLINKSCAS:26093-31-2",
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"PubChem:4580",
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"ChEBI:51771",
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"ChEMBL:CHEMBL270672",
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"KNApSAcK:C00048593",
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"PDB-CCD:MCM",
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],
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)
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def test_irregular(self):
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"""compound.irregular tests."""
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with open("KEGG/compound.irregular") as handle:
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records = list(Compound.parse(handle))
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self.assertEqual(len(records), 2)
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self.assertEqual(records[0].entry, "C01454")
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def test_mass(self):
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"""record.mass tests."""
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with open("KEGG/compound.sample") as handle:
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records = list(Compound.parse(handle))
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self.assertEqual(records[0].entry, "C00023")
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self.assertEqual(records[0].mass, "55.9349")
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self.assertEqual(records[2].entry, "C00099")
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self.assertEqual(records[2].mass, "89.0477")
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self.assertEqual(records[3].entry, "C00294")
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self.assertEqual(records[3].mass, "268.0808")
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class MapTests(unittest.TestCase):
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"""Bio.KEGG.Map tests."""
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def test_map00950(self):
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"""map00950.rea tests."""
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system = System()
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with open("KEGG/map00950.rea") as handle:
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for reaction in Map.parse(handle):
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system.add_reaction(reaction)
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rxs = system.reactions()
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self.assertEqual(len(rxs), 56)
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# sort the reaction output by the string names, so that the
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# output will be consistent between python versions
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rxs.sort(key=lambda x: str(x)) # noqa: E731
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self.assertEqual(
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str(rxs[0]),
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"(R)-N-Methylcoclaurine + (S)-Coclaurine + NADPH + O2 "
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"<=> 2'-Norberbamunine + 2 H2O + NADP",
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)
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self.assertEqual(str(rxs[-1]), "Tyramine <=> Dopamine")
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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