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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 StringIO import *
from Bio.SCOP import *
import sys
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 'test'
tests = [AstralTests]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
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):
assert self.astral.getSeqBySid('d3sdha_').data == "AAAAA"
assert self.astral.getSeqBySid('d4hbib_').data == "KKKKK"
dom = self.scop.getDomainBySid('d3sdha_')
assert self.astral.getSeq(dom).data == "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")
assert astral.getSeqBySid('d3sdha_').data == "AAAAA"
assert astral.getSeqBySid('d4hbib_').data == "KKKKK"
def testGetDomainsFromFile(self):
filename = "SCOP/scopseq-test/astral-scopdom-seqres-sel-gs-bib-20-test.id"
domains = self.astral.getAstralDomainsFromFile(filename)
assert len(domains)==3
assert domains[0].sid == "d3sdha_"
assert domains[1].sid == "d4hbib_"
assert domains[2].sid == "d5hbia_"
def testGetDomainsClustered(self):
domains1 = self.astral.domainsClusteredById(20)
assert len(domains1) == 3
assert domains1[0].sid == "d3sdha_"
assert domains1[1].sid == "d4hbib_"
assert domains1[2].sid == "d5hbia_"
domains2 = self.astral.domainsClusteredByEv(1e-15)
assert len(domains2) == 1
#d1 = scop.getDomainBySid("d3sdha_")
#assert d1.isIn(astral.getHashedDomainsClusteredByPercentId(20))
#assert d1.isIn(astral.getHashedDomainsClusteredByEv(-15))
if __name__ == '__main__':
unittest.main()
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