Exemple #1
0
 def test_missing_tips(self):
     ds1 = dendropy.DataSet()
     ds1.read_from_string(('>a\n'
                           'ATCG\n'
                           '>b\n'
                           'ATCG\n'
                           '>c\n'
                           'ATCG\n'
                           '>d\n'
                           'ATCG\n'),
                          schema='fasta',
                          data_type='dna')
     ds2 = dendropy.DataSet()
     tree_str = '((a,b),c);'
     ds2.read_from_string(tree_str, schema='newick')
     extra, missing = treeholder.check_taxon_labels(
         ds2.tree_lists[-1].taxon_set, ds1)
     self.assertEqual(len(missing), 1)
     self.assertEqual(len(extra), 0)
     self.assertEqual(missing[0], 'd')
     tree_stream = StringIO()
     tree_stream.write(tree_str)
     self.assertRaises(TaxaLabelsMismatchError,
                       treeholder.read_trees_into_dataset,
                       ds1,
                       tree_stream,
                       starting_tree=True)
Exemple #2
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 def test_missing_tips(self):
     ds1 = dendropy.DataSet()
     ds1.read_from_string(
             ('>a\n'
              'ATCG\n'
              '>b\n'
              'ATCG\n'
              '>c\n'
              'ATCG\n'
              '>d\n'
              'ATCG\n'),
             schema='fasta',
             data_type='dna')
     ds2 = dendropy.DataSet()
     tree_str = '((a,b),c);'
     ds2.read_from_string(
             tree_str,
             schema='newick')
     extra, missing = treeholder.check_taxon_labels(
             ds2.tree_lists[-1].taxon_set, ds1)
     self.assertEqual(len(missing), 1)
     self.assertEqual(len(extra), 0)
     self.assertEqual(missing[0], 'd')
     tree_stream = StringIO()
     tree_stream.write(tree_str)
     self.assertRaises(TaxaLabelsMismatchError,
             treeholder.read_trees_into_dataset,
             ds1, tree_stream, starting_tree=True)
Exemple #3
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 def test_match(self):
     ds1 = dendropy.DataSet()
     ds1.read_from_string(('>a\n'
                           'ATCG\n'
                           '>b\n'
                           'ATCG\n'
                           '>c\n'
                           'ATCG\n'),
                          schema='fasta',
                          data_type='dna')
     ds2 = dendropy.DataSet()
     tree_str = '((a,b),c);'
     ds2.read_from_string(tree_str, schema='newick')
     extra, missing = treeholder.check_taxon_labels(
         ds2.tree_lists[-1].taxon_set, ds1)
     self.assertEqual(len(missing), 0)
     self.assertEqual(len(extra), 0)
Exemple #4
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 def test_match(self):
     ds1 = dendropy.DataSet()
     ds1.read_from_string(
             ('>a\n'
              'ATCG\n'
              '>b\n'
              'ATCG\n'
              '>c\n'
              'ATCG\n'),
             schema='fasta',
             data_type='dna')
     ds2 = dendropy.DataSet()
     tree_str = '((a,b),c);'
     ds2.read_from_string(
             tree_str,
             schema='newick')
     extra, missing = treeholder.check_taxon_labels(
             ds2.tree_lists[-1].taxon_set, ds1)
     self.assertEqual(len(missing), 0)
     self.assertEqual(len(extra), 0)