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import sys
import unittest
from ost.seq.alg import aaindex
class TestAAIndex(unittest.TestCase):
def testStuff(self):
index = aaindex.AAIndex()
# test some random aaindex annotations from all three files
# the files themselves are lazy loaded until the required
# annotation is found
# entry from aaindex1
self.assertEqual(index["BHAR880101"].GetScore("C"), 0.346)
# entries from aaindex2
# symmetric one:
self.assertEqual(index["HENS920102"].GetPairScore("C", "A"), -1.0)
self.assertEqual(index["HENS920102"].GetPairScore("A", "C"), -1.0)
# non-symmetric one:
self.assertEqual(index["LINK010101"].GetPairScore("C", "A"), 0.035)
self.assertEqual(index["LINK010101"].GetPairScore("A", "C"), 0.000)
# entries from aaindex3
# symmetric one
self.assertEqual(index["TANS760102"].GetPairScore("H", "R"), 17)
self.assertEqual(index["TANS760102"].GetPairScore("R", "H"), 17)
# non symmetric one
self.assertEqual(index["ZHAC000102"].GetPairScore("H", "R"), 2.19)
self.assertEqual(index["ZHAC000102"].GetPairScore("R", "H"), 0.94)
# depending on annotation type (single amino acids or pairs), we need
# to call the right functions
with self.assertRaises(RuntimeError):
index["TANS760102"].GetScore("H")
with self.assertRaises(RuntimeError):
index["BHAR880101"].GetPairScore("H", "R")
if __name__ == "__main__":
from ost import testutils
# the function below indirectly enables GetSharedDataPath when
# calling stuff from python which is the case in unit tests
testutils.DefaultCompoundLibIsSet()
testutils.RunTests()
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