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