Python reference_single_taxonset_dataset Examples

Example #1

File: test_datagen.py Project: BioinformaticsArchive/DendroPy

 def testReferenceSingleTaxonSetDataSet(self):
     dataset = datagen.reference_single_taxonset_dataset()
     self.assertEqual(len(dataset.taxon_sets), 1)
     self.assertEqual(len(dataset.taxon_sets[0]), 33)
     self.assertEqual(len(dataset.tree_lists), 1)
     self.assertIs(dataset.tree_lists[0].taxon_set, dataset.taxon_sets[0])
     self.assertEqual(len(dataset.char_matrices), 2)
     self.assertIs(dataset.char_matrices[0].taxon_set, dataset.taxon_sets[0])
     self.assertIs(dataset.char_matrices[1].taxon_set, dataset.taxon_sets[0])

Example #2

File: test_datagen.py Project: nesnidal/DendroPy

 def testReferenceSingleTaxonSetDataSet(self):
     dataset = datagen.reference_single_taxonset_dataset()
     self.assertEqual(len(dataset.taxon_sets), 1)
     self.assertEqual(len(dataset.taxon_sets[0]), 33)
     self.assertEqual(len(dataset.tree_lists), 1)
     self.assertIs(dataset.tree_lists[0].taxon_set, dataset.taxon_sets[0])
     self.assertEqual(len(dataset.char_matrices), 2)
     self.assertIs(dataset.char_matrices[0].taxon_set,
                   dataset.taxon_sets[0])
     self.assertIs(dataset.char_matrices[1].taxon_set,
                   dataset.taxon_sets[0])

Example #3

 def setUp(self):
     self.reference_dataset = datagen.reference_single_taxonset_dataset()
     self.data_path = pathmap.named_output_path("char_read.nex")
     self.reference_dataset.write_to_path(self.data_path, "nexus")

Example #4

File: test_dataio_nexus.py Project: jjhoyt/gengis

 def testRoundTripReference(self):
     reference_dataset = datagen.reference_single_taxonset_dataset()
     self.roundTripDataSetTest(reference_dataset, "nexus")

Example #5

File: test_dataio_nexml.py Project: BioinformaticsArchive/DendroPy

 def testRoundTripReference(self):
     reference_dataset = datagen.reference_single_taxonset_dataset()
     self.roundTripDataSetTest(reference_dataset, "nexml", ignore_taxon_order=True, ignore_chartypes=True)

Example #6

 def testRoundTripReference(self):
     reference_dataset = datagen.reference_single_taxonset_dataset()
     self.roundTripDataSetTest(reference_dataset,
                               "nexml",
                               ignore_taxon_order=True)

Example #7

File: test_dataobject_char_array.py Project: BioinformaticsArchive/DendroPy

 def setUp(self):
     self.reference_dataset = datagen.reference_single_taxonset_dataset()
     self.data_path = pathmap.named_output_path("char_read.nex")
     self.reference_dataset.write_to_path(self.data_path, "nexus")

Example #8

File: test_dataobject_dataset.py Project: emilhaegglund/wgfast

 def setUp(self):
     self.dataset = datagen.reference_single_taxonset_dataset()

Example #9

File: test_dataobject_dataset.py Project: BioinformaticsArchive/DendroPy

 def setUp(self):
     self.dataset = datagen.reference_single_taxonset_dataset()

Example #10

 def testRoundTripReference(self):
     reference_dataset = datagen.reference_single_taxonset_dataset()
     self.roundTripDataSetTest(reference_dataset, "nexus")