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import unittest
from ost import *
from ost import settings
from ost import seq
from ost.bindings.clustalw import *
class TestSemiGlobalAlign(unittest.TestCase):
def testSemiGlobalAlignment(self):
seq_a=seq.CreateSequence('A', 'abcdefghijklmnok')
seq_b=seq.CreateSequence('B', 'cdehijk')
alns=seq.alg.SemiGlobalAlign(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]), 'abcdefghijklmnok')
self.assertEqual(str(alns[0].sequences[1]), '--cde--hijk-----')
self.assertEqual(alns[0].sequences[0].offset, 0)
self.assertEqual(alns[0].sequences[1].offset, 0)
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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