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)
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)
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)
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)