def testBoundTaxonNamespaceDefault(self):
d = dendropy.DataSet()
t = dendropy.TaxonNamespace()
d.attach_taxon_namespace(t)
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertIs(d.taxon_namespaces[0], d.attached_taxon_namespace)
d.read(path=pathmap.mixed_source_path(
'reference_single_taxonset_dataset.nex'),
schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.mle.nex'),
schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(
path=pathmap.tree_source_path('pythonidae.reference-trees.newick'),
schema="newick")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.char_source_path('caenophidia_mos.chars.fasta'),
schema="fasta",
data_type="protein")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 147)
def testBindAndUnbind(self):
d = dendropy.DataSet(attach_taxon_set=True)
self.assertEqual(len(d.taxon_sets), 1)
self.assertIs(d.taxon_sets[0], d.attached_taxon_set)
d.read_from_path(
pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'),
"nexus")
_LOG.info(d.taxon_sets[0].description(2))
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'),
"nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(
pathmap.tree_source_path('pythonidae.reference-trees.newick'),
"newick")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.detach_taxon_set()
d.read_from_path(
pathmap.char_source_path('caenophidia_mos.chars.fasta'),
"proteinfasta")
self.assertEqual(len(d.taxon_sets), 2)
self.assertEqual(len(d.taxon_sets[0]), 33)
self.assertEqual(len(d.taxon_sets[1]), 114)
def testAttachTaxonNamespaceOnGet(self):
t = dendropy.TaxonNamespace()
d = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'),
"nexus",
taxon_namespace=t)
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertIsNot(d.attached_taxon_namespace, None)
self.assertIs(d.taxon_namespaces[0], d.attached_taxon_namespace)
self.assertIs(d.attached_taxon_namespace, t)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.mle.nex'),
schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(
path=pathmap.tree_source_path('pythonidae.reference-trees.newick'),
schema="newick")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.detach_taxon_namespace()
d.read_from_path(
pathmap.char_source_path('caenophidia_mos.chars.fasta'),
schema="fasta",
data_type="protein")
self.assertEqual(len(d.taxon_namespaces), 2)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
self.assertEqual(len(d.taxon_namespaces[1]), 114)
def test_attached_taxon_namespace(self):
tns = dendropy.TaxonNamespace()
ds = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'),
"nexus",
taxon_namespace=tns)
self.verify_attached_taxon_namespace(ds, tns)
def test_attached_taxon_namespace(self):
d0 = dendropy.DataSet.get_from_path(pathmap.mixed_source_path("multitaxa_mesquite.nex"), "nexus")
for tns in d0.taxon_namespaces:
d0.attach_taxon_namespace(tns)
s = self.write_out_validate_equal_and_return(d0, "nexus", {})
ds = dendropy.DataSet.get_from_string(s, "nexus")
self.verify_attached_taxon_namespace_written(ds, tns)
def testBindToSpecifiedTaxonSet(self):
d = dendropy.DataSet()
t = dendropy.TaxonSet()
d.attach_taxon_set(t)
self.assertEqual(len(d.taxon_sets), 1)
self.assertIs(d.taxon_sets[0], d.attached_taxon_set)
self.assertIs(d.attached_taxon_set, t)
d.read_from_path(
pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'),
"nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'),
"nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(
pathmap.tree_source_path('pythonidae.reference-trees.newick'),
"newick")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.detach_taxon_set()
d.read_from_path(
pathmap.char_source_path('caenophidia_mos.chars.fasta'),
"proteinfasta")
self.assertEqual(len(d.taxon_sets), 2)
self.assertEqual(len(d.taxon_sets[0]), 33)
self.assertEqual(len(d.taxon_sets[1]), 114)
def test_attached_taxon_namespace(self):
tns = dendropy.TaxonNamespace()
ds = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'),
"nexus",
taxon_namespace=tns)
self.verify_attached_taxon_namespace(ds, tns)
def test_basic_get(self):
src_filename = "standard-test-mixed.1.basic.nexus"
src_path = pathmap.mixed_source_path(src_filename)
ds = dendropy.DataSet.get_from_path(
src_path,
"nexus",
suppress_internal_node_taxa=False, # so internal labels get translated
)
self.verify_dataset(ds)
def test_default(self):
d0 = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'), "nexus")
s = self.write_out_validate_equal_and_return(d0, "nexus", {})
ds = dendropy.DataSet.get_from_string(
s,
"nexus",
)
self.verify_unrestricted(ds)
def test_basic_get(self):
src_filename = "standard-test-mixed.1.basic.nexus"
src_path = pathmap.mixed_source_path(src_filename)
ds = dendropy.DataSet.get_from_path(
src_path,
"nexus",
suppress_internal_node_taxa=
False, # so internal labels get translated
)
self.verify_dataset(ds)
def test_basic_read(self):
src_filename = "standard-test-mixed.1.basic.nexus"
src_path = pathmap.mixed_source_path(src_filename)
ds = dendropy.DataSet()
result = ds.read(
path=src_path,
schema="nexus",
suppress_internal_node_taxa=False, # so internal labels get translated
)
self.assertEqual(result, (1, 7, 4))
self.verify_dataset(ds)
def test_attached_taxon_namespace(self):
d0 = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'), "nexus")
for tns in d0.taxon_namespaces:
d0.attach_taxon_namespace(tns)
s = self.write_out_validate_equal_and_return(d0, "nexus", {})
ds = dendropy.DataSet.get_from_string(
s,
"nexus",
)
self.verify_attached_taxon_namespace_written(ds, tns)
def test_basic_read(self):
src_filename = "standard-test-mixed.1.basic.nexus"
src_path = pathmap.mixed_source_path(src_filename)
ds = dendropy.DataSet()
result = ds.read(
path=src_path,
schema="nexus",
suppress_internal_node_taxa=
False, # so internal labels get translated
)
self.assertEqual(result, (1, 7, 4))
self.verify_dataset(ds)
def testMultiTaxonNamespace(self):
d = dendropy.DataSet()
d.read(path=pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'), schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.mle.nex'), schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 2)
self.assertEqual(len(d.taxon_namespaces[1]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.reference-trees.newick'), schema="newick")
self.assertEqual(len(d.taxon_namespaces), 3)
self.assertEqual(len(d.taxon_namespaces[2]), 33)
d.read(path=pathmap.char_source_path('caenophidia_mos.chars.fasta'), schema="fasta", data_type="protein")
self.assertEqual(len(d.taxon_namespaces), 4)
self.assertEqual(len(d.taxon_namespaces[3]), 114)
def testMultiTaxonSet(self):
d = dendropy.DataSet()
d.read_from_path(pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'), "nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'), "nexus")
self.assertEqual(len(d.taxon_sets), 2)
self.assertEqual(len(d.taxon_sets[1]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.reference-trees.newick'), "newick")
self.assertEqual(len(d.taxon_sets), 3)
self.assertEqual(len(d.taxon_sets[2]), 33)
d.read_from_path(pathmap.char_source_path('caenophidia_mos.chars.fasta'), "proteinfasta")
self.assertEqual(len(d.taxon_sets), 4)
self.assertEqual(len(d.taxon_sets[3]), 114)
def testBoundTaxonSetDefault(self):
d = dendropy.DataSet(attach_taxon_set=True)
self.assertEqual(len(d.taxon_sets), 1)
self.assertIs(d.taxon_sets[0], d.attached_taxon_set)
d.read_from_path(pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'), "nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'), "nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.reference-trees.newick'), "newick")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.char_source_path('caenophidia_mos.chars.fasta'), "proteinfasta")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 147)
def testBoundTaxonNamespaceDefault(self):
d = dendropy.DataSet()
t = dendropy.TaxonNamespace()
d.attach_taxon_namespace(t)
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertIs(d.taxon_namespaces[0], d.attached_taxon_namespace)
d.read(path=pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'), schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.mle.nex'), schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.reference-trees.newick'), schema="newick")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.char_source_path('caenophidia_mos.chars.fasta'), schema="fasta", data_type="protein")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 147)
def testBindAndUnbind(self):
d = dendropy.DataSet(attach_taxon_set=True)
self.assertEqual(len(d.taxon_sets), 1)
self.assertIs(d.taxon_sets[0], d.attached_taxon_set)
d.read_from_path(pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'), "nexus")
_LOG.info(d.taxon_sets[0].description(2))
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'), "nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.reference-trees.newick'), "newick")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.detach_taxon_set()
d.read_from_path(pathmap.char_source_path('caenophidia_mos.chars.fasta'), "proteinfasta")
self.assertEqual(len(d.taxon_sets), 2)
self.assertEqual(len(d.taxon_sets[0]), 33)
self.assertEqual(len(d.taxon_sets[1]), 114)
def testBindToSpecifiedTaxonSet(self):
d = dendropy.DataSet()
t = dendropy.TaxonSet()
d.attach_taxon_set(t)
self.assertEqual(len(d.taxon_sets), 1)
self.assertIs(d.taxon_sets[0], d.attached_taxon_set)
self.assertIs(d.attached_taxon_set, t)
d.read_from_path(pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'), "nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'), "nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.reference-trees.newick'), "newick")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.detach_taxon_set()
d.read_from_path(pathmap.char_source_path('caenophidia_mos.chars.fasta'), "proteinfasta")
self.assertEqual(len(d.taxon_sets), 2)
self.assertEqual(len(d.taxon_sets[0]), 33)
self.assertEqual(len(d.taxon_sets[1]), 114)
def testMultiTaxonNamespace(self):
d = dendropy.DataSet()
d.read(path=pathmap.mixed_source_path(
'reference_single_taxonset_dataset.nex'),
schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.mle.nex'),
schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 2)
self.assertEqual(len(d.taxon_namespaces[1]), 33)
d.read(
path=pathmap.tree_source_path('pythonidae.reference-trees.newick'),
schema="newick")
self.assertEqual(len(d.taxon_namespaces), 3)
self.assertEqual(len(d.taxon_namespaces[2]), 33)
d.read(path=pathmap.char_source_path('caenophidia_mos.chars.fasta'),
schema="fasta",
data_type="protein")
self.assertEqual(len(d.taxon_namespaces), 4)
self.assertEqual(len(d.taxon_namespaces[3]), 114)
def testAttachTaxonNamespaceOnGet(self):
t = dendropy.TaxonNamespace()
d = dendropy.DataSet.get_from_path(pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'),
"nexus",
taxon_namespace=t)
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertIsNot(d.attached_taxon_namespace, None)
self.assertIs(d.taxon_namespaces[0], d.attached_taxon_namespace)
self.assertIs(d.attached_taxon_namespace, t)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.mle.nex'), schema="nexus")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.read(path=pathmap.tree_source_path('pythonidae.reference-trees.newick'), schema="newick")
self.assertEqual(len(d.taxon_namespaces), 1)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
d.detach_taxon_namespace()
d.read_from_path(pathmap.char_source_path('caenophidia_mos.chars.fasta'), schema="fasta", data_type="protein")
self.assertEqual(len(d.taxon_namespaces), 2)
self.assertEqual(len(d.taxon_namespaces[0]), 33)
self.assertEqual(len(d.taxon_namespaces[1]), 114)
def testMultiTaxonSet(self):
d = dendropy.DataSet()
d.read_from_path(
pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'),
"nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'),
"nexus")
self.assertEqual(len(d.taxon_sets), 2)
self.assertEqual(len(d.taxon_sets[1]), 33)
d.read_from_path(
pathmap.tree_source_path('pythonidae.reference-trees.newick'),
"newick")
self.assertEqual(len(d.taxon_sets), 3)
self.assertEqual(len(d.taxon_sets[2]), 33)
d.read_from_path(
pathmap.char_source_path('caenophidia_mos.chars.fasta'),
"proteinfasta")
self.assertEqual(len(d.taxon_sets), 4)
self.assertEqual(len(d.taxon_sets[3]), 114)
def testBoundTaxonSetDefault(self):
d = dendropy.DataSet(attach_taxon_set=True)
self.assertEqual(len(d.taxon_sets), 1)
self.assertIs(d.taxon_sets[0], d.attached_taxon_set)
d.read_from_path(
pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'),
"nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(pathmap.tree_source_path('pythonidae.mle.nex'),
"nexus")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(
pathmap.tree_source_path('pythonidae.reference-trees.newick'),
"newick")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 33)
d.read_from_path(
pathmap.char_source_path('caenophidia_mos.chars.fasta'),
"proteinfasta")
self.assertEqual(len(d.taxon_sets), 1)
self.assertEqual(len(d.taxon_sets[0]), 147)
def test_default(self):
d0 = dendropy.DataSet.get_from_path(pathmap.mixed_source_path("multitaxa_mesquite.nex"), "nexus")
s = self.write_out_validate_equal_and_return(d0, "nexus", {})
ds = dendropy.DataSet.get_from_string(s, "nexus")
self.verify_unrestricted(ds)
def get_source_dataset(self, **kwargs):
src_ds = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path("standard-test-mixed.1.basic.nexus"),
"nexus", **kwargs)
return src_ds
def testFromPathFactory(self):
ds2 = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'),
"nexus")
self.assertDistinctButEqual(self.dataset, ds2, ignore_chartypes=True)
def test_default(self):
ds = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'),
"nexus")
self.verify_unrestricted(ds)
def testFromPathFactory(self):
ds2 = dendropy.DataSet.get_from_path(pathmap.mixed_source_path('reference_single_taxonset_dataset.nex'), "nexus")
self.assertDistinctButEqual(self.dataset, ds2,
ignore_chartypes=True)
def test_default(self):
ds = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path('multitaxa_mesquite.nex'), "nexus")
self.verify_unrestricted(ds)
def get_source_dataset(self, **kwargs):
src_ds = dendropy.DataSet.get_from_path(
pathmap.mixed_source_path("standard-test-mixed.1.basic.nexus"), "nexus", **kwargs
)
return src_ds
