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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
61 lines
2.2 KiB
Python
61 lines
2.2 KiB
Python
# Copyright 2001 by Gavin E. Crooks. 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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"""Unit test for Astral."""
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import unittest
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from Bio.SCOP import Astral
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from Bio.SCOP import Scop
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class AstralTests(unittest.TestCase):
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def setUp(self):
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self.scop = Scop(dir_path="SCOP", version="test")
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self.astral = Astral(scop=self.scop, dir_path="SCOP", version="test")
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def testGetSeq(self):
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self.assertEqual(self.astral.getSeqBySid("d3sdha_"), "AAAAA")
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self.assertEqual(self.astral.getSeqBySid("d4hbib_"), "KKKKK")
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dom = self.scop.getDomainBySid("d3sdha_")
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self.assertEqual(self.astral.getSeq(dom), "AAAAA")
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def testConstructWithCustomFile(self):
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scop = Scop(dir_path="SCOP", version="test")
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astral = Astral(
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scop=scop, astral_file="SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa"
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)
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self.assertEqual(astral.getSeqBySid("d3sdha_"), "AAAAA")
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self.assertEqual(astral.getSeqBySid("d4hbib_"), "KKKKK")
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def testGetDomainsFromFile(self):
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filename = "SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-20-test.id"
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domains = self.astral.getAstralDomainsFromFile(filename)
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self.assertEqual(len(domains), 3)
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self.assertEqual(domains[0].sid, "d3sdha_")
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self.assertEqual(domains[1].sid, "d4hbib_")
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self.assertEqual(domains[2].sid, "d5hbia_")
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def testGetDomainsClustered(self):
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domains1 = self.astral.domainsClusteredById(20)
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self.assertEqual(len(domains1), 3)
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self.assertEqual(domains1[0].sid, "d3sdha_")
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self.assertEqual(domains1[1].sid, "d4hbib_")
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self.assertEqual(domains1[2].sid, "d5hbia_")
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domains2 = self.astral.domainsClusteredByEv(1e-15)
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self.assertEqual(len(domains2), 1)
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# d1 = scop.getDomainBySid("d3sdha_")
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# self.assertEqual(d1.isIn(astral.getHashedDomainsClusteredByPercentId(20))
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# self.assertEqual(d1.isIn(astral.getHashedDomainsClusteredByEv(-15))
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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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