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import unittest
import os
import ost
from ost import seq, io, mol
class TestAlignmentFromChainView(unittest.TestCase):
def testAlignment(self):
prot = io.LoadPDB(os.path.join("testfiles", "dummy.pdb"))
view_resnums = [2,3,4,7,8]
query = "rnum=" + ','.join([str(item) for item in view_resnums])
prot_view = prot.Select(query)
exp_handle_seq = ''.join([r.one_letter_code for r in prot.residues])
exp_view_seq = ['-'] * len(prot.residues)
for rnum in view_resnums:
exp_view_seq[rnum-1] = prot.residues[rnum-1].one_letter_code
exp_view_seq = ''.join(exp_view_seq)
aln = seq.alg.AlignmentFromChainView(prot_view.chains[0],
handle_seq_name='custom_handle_name',
view_seq_name='custom_view_name')
handle_seq = aln.GetSequence(0)
view_seq = aln.GetSequence(1)
self.assertEqual(handle_seq.GetName(), 'custom_handle_name')
self.assertEqual(view_seq.GetName(), 'custom_view_name')
self.assertEqual(exp_handle_seq, handle_seq.GetString())
self.assertEqual(exp_view_seq, view_seq.GetString())
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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