tests/translationDB_test.py

   1 import unittest
   2
   3 from testlib import testutil, PygrTestProgram
   4 from pygr import translationDB, seqdb
   5
   6 class TranslationDB_Test(unittest.TestCase):
   7     def setUp(self):
   8         hbb1_mouse = testutil.datafile('hbb1_mouse.fa')
   9         self.dna = seqdb.SequenceFileDB(hbb1_mouse)
  10         self.tdb = translationDB.get_translation_db(self.dna)
  11
  12     def test_basic_slice(self):
  13         id = 'gi|171854975|dbj|AB364477.1|'
  14         tseq = self.tdb[id][0:99]
  15         assert str(tseq)[0:10] == 'MVHLTDAEKA'
  16
  17         tseq = self.tdb[id][1:100]
  18         assert str(tseq)[0:10] == 'WCT*LMLRRL'
  19
  20     def test_slice_empty_stop(self):
  21         id = 'gi|171854975|dbj|AB364477.1|'
  22         tseq = self.tdb[id][0:]
  23         assert str(tseq)[0:10] == 'MVHLTDAEKA'
  24
  25         tseq = self.tdb[id][1:]
  26         assert str(tseq)[0:10] == 'WCT*LMLRRL'
  27
  28     def test_slice_empty_start(self):
  29         id = 'gi|171854975|dbj|AB364477.1|'
  30         tseq = self.tdb[id][:99]
  31         assert str(tseq)[0:10] == 'MVHLTDAEKA'
  32
  33     def test_repr_ne(self):
  34         """
  35         Make sure there's some way to distinguish translated seqs from
  36         regular, visually!
  37         """
  38         id = 'gi|171854975|dbj|AB364477.1|'
  39
  40         seq = self.dna[id]
  41         tseq = self.tdb[id]
  42
  43         assert repr(seq) != repr(tseq)
  44
  45     def test_invalid_annodb_key_str(self):
  46         """
  47         The invalid key should be mentioned in the KeyError...
  48         """
  49         try:
  50             self.tdb.annodb['fooBar']
  51             assert 0, "should not reach this point"
  52         except KeyError, e:
  53             assert 'fooBar' in str(e)
  54
  55 if __name__ == '__main__':
  56     PygrTestProgram(verbosity=2)