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import unittest
from ost import *
from ost import settings
from ost import seq
from ost.bindings.clustalw import *
class TestLocalAlign(unittest.TestCase):
def testDeletionInSeqB(self):
seq_a=seq.CreateSequence('A', 'acdefghiklmn')
seq_b=seq.CreateSequence('B', 'acdhiklmn')
alns=seq.alg.LocalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
self.assertEqual(len(alns), 1)
self.assertEqual(alns[0].sequences[0].name, 'A')
self.assertEqual(alns[0].sequences[1].name, 'B')
self.assertEqual(str(alns[0].sequences[0]), 'acdefghiklmn')
self.assertEqual(str(alns[0].sequences[1]), 'acd---hiklmn')
self.assertEqual(alns[0].sequences[0].offset, 0)
self.assertEqual(alns[0].sequences[1].offset, 0)
def testDeletionInSeqA(self):
seq_a=seq.CreateSequence('A', 'acdhiklmn')
seq_b=seq.CreateSequence('B', 'acdefghiklmn')
alns=seq.alg.LocalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
self.assertEqual(len(alns), 1)
self.assertEqual(alns[0].sequences[0].name, 'A')
self.assertEqual(alns[0].sequences[1].name, 'B')
self.assertEqual(str(alns[0].sequences[0]), 'acd---hiklmn')
self.assertEqual(str(alns[0].sequences[1]), 'acdefghiklmn')
self.assertEqual(alns[0].sequences[0].offset, 0)
self.assertEqual(alns[0].sequences[1].offset, 0)
def testOffset(self):
seq_a=seq.CreateSequence('A', 'acdhiklmn')
seq_b=seq.CreateSequence('B', 'ggiklmn')
alns=seq.alg.LocalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
self.assertEqual(len(alns), 1)
self.assertEqual(alns[0].sequences[0].name, 'A')
self.assertEqual(alns[0].sequences[1].name, 'B')
self.assertEqual(str(alns[0].sequences[0]), 'iklmn')
self.assertEqual(str(alns[0].sequences[1]), 'iklmn')
self.assertEqual(alns[0].sequences[0].offset, 4)
self.assertEqual(alns[0].sequences[1].offset, 2)
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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