text: #!/usr/bin/env python
   
  #  Copyright (c) 2006, The Regents of the University of California, through 
  #  Lawrence Berkeley National Laboratory (subject to receipt of any required
  #  approvals from the U.S. Dept. of Energy).  All rights reserved.
  
  #  This software is distributed under the new BSD Open Source License.
  #  <http://www.opensource.org/licenses/bsd-license.html>
  #
  #  Redistribution and use in source and binary forms, with or without 
  #  modification, are permitted provided that the following conditions are met: 
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  #  notice, this list of conditions and the following disclaimer in the 
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  #  National Laboratory, U.S. Dept. of Energy nor the names of its contributors 
  #  may be used to endorse or promote products derived from this software 
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  from corebio import *
  from corebio.seq import *
  from corebio.seq_io import *
  from test_corebio import *
  from corebio.seq_io import phylip_io
  
  from corebio._py3k import StringIO
  
  import unittest
  
  class test_phylip_io(unittest.TestCase) :
  
      def test_read(self) :
          f = testdata_stream("phylip_test_1.phy")
          seqs = phylip_io.read(f)
          #print seqs
          self.assertEqual(len(seqs), 10)
          self.assertEqual(seqs[0].name, "Cow")
          self.assertEqual(len(seqs[1]), 234)
          f.close()
      
      def test_parse_plain_fail(self) :
          # should fail with parse error
          f = StringIO(plain_io.example)
          self.assertRaises(ValueError, 
              phylip_io.read, f  )
      
      def test_parse_phylip_test_2(self):
          f = testdata_stream('phylip_test_2.phy')
          seqs = phylip_io.read(f)
          self.assertEqual(len(seqs), 6)
          self.assertEqual(len(seqs[0]), 20)
          self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
          self.assertEqual(seqs[1].name, "Hesperorni")
          f.close()
      
      def test_parse_clustal_fail(self) :
          # should fail with parse error
          f = StringIO(clustal_io.example)
          self.assertRaises(ValueError, 
              phylip_io.read, f , protein_alphabet )
      
      def test_parse_phylip_test_3(self):
          f = testdata_stream('phylip_test_3.phy')
          seqs = phylip_io.read(f)
          self.assertEqual(len(seqs), 6)
          self.assertEqual(len(seqs[0]), 20)
          self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
          self.assertEqual(seqs[1].name, "Hesperorni")
          f.close()
      
      def test_parse_phylip_test_4(self):
          f = testdata_stream('phylip_test_4.phy')
          seqs = phylip_io.read(f)
          self.assertEqual(len(seqs), 6)
          self.assertEqual(len(seqs[0]), 25)
          self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
          self.assertEqual(seqs[2].name, "ddrasa")
          f.close()
      
      
      def test_parse_phylip_test_5(self):
          f = testdata_stream('phylip_test_5.phy')
          seqs = phylip_io.read(f)
          self.assertEqual(len(seqs), 6)
          self.assertEqual(len(seqs[0]), 50)
          self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG")
          self.assertEqual(seqs[2].name, "ddrasa")
          f.close()
          
      def test_parse_wrong_phylip_codes_1(self):
          f = testdata_stream('phylip_test_6.corrupt.phy')
          self.assertRaises(ValueError, 
              phylip_io.read, f , protein_alphabet )
          f.close()
          
      def test_parse_wrong_phylip_codes_2(self):
          f = testdata_stream('phylip_test_7.corrupt.phy')
          self.assertRaises(ValueError, 
              phylip_io.read, f , protein_alphabet )
          f.close()
  
      def test_parse_phylip_dna(self):
          f = testdata_stream('dna.phy')
          seqs = phylip_io.read(f)
          self.assertEqual(len(seqs), 10)
          self.assertEqual(len(seqs[0]), 705)
          self.assertEqual( str(seqs[1][0:10]), "ATGGCACACC")
          self.assertEqual(seqs[2].name, "Chicken")
          f.close()
     
               
  if __name__ == '__main__':
      unittest.main()
  