def testReadingAndWritingCharMatrix(self):
dna1 = datagen.reference_dna_matrix()
output_path = pathmap.named_output_path(
filename="roundtrip_test.fasta", suffix_timestamp=True)
dna1.write_to_path(output_path, 'fasta')
dna2 = dendropy.DnaCharacterMatrix.get_from_path(output_path, 'fasta')
self.assertDistinctButEqual(dna1, dna2)
def testWriteTreeListSameTaxa(self):
output_path = pathmap.named_output_path(filename="reference.trees.out.newick", suffix_timestamp=True)
self.ref_tree_list.write_to_path(output_path, schema="newick")
t_tree_list = dendropy.TreeList.get_from_path(output_path, "newick", taxon_set=self.ref_tree_list.taxon_set)
self.assertDistinctButEqualTreeList(
self.ref_tree_list,
t_tree_list,
distinct_taxa=False,
equal_oids=None)
def testWriteTreeListDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
output_path = pathmap.named_output_path(filename="reference.trees.out.nexus", suffix_timestamp=True)
ref_tree_list.write_to_path(output_path, "nexus")
t_tree_list = dendropy.TreeList.get_from_path(output_path, "nexus")
self.assertDistinctButEqualTreeList(
ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None)
def testWriteTreeListSameTaxa(self):
output_path = pathmap.named_output_path(
filename="reference.trees.out.newick", suffix_timestamp=True)
self.ref_tree_list.write_to_path(output_path, schema="newick")
t_tree_list = dendropy.TreeList.get_from_path(
output_path, "newick", taxon_set=self.ref_tree_list.taxon_set)
self.assertDistinctButEqualTreeList(self.ref_tree_list,
t_tree_list,
distinct_taxa=False,
equal_oids=None)
def testWriteTreeListDistinctTaxa(self):
ref_tree_list = datagen.reference_tree_list()
output_path = pathmap.named_output_path(
filename="reference.trees.out.nexus", suffix_timestamp=True)
ref_tree_list.write_to_path(output_path, "nexus")
t_tree_list = dendropy.TreeList.get_from_path(output_path, "nexus")
self.assertDistinctButEqualTreeList(ref_tree_list,
t_tree_list,
distinct_taxa=True,
equal_oids=None)
def testDnaRountTripDistinctTaxa(self):
c1 = datagen.reference_dna_matrix()
path = pathmap.named_output_path("char_rw_dna.nex")
c1.write_to_path(path, "nexus")
c2 = dendropy.DnaCharacterMatrix.get_from_path(path, "nexus")
self.assertDistinctButEqual(c1,
c2,
char_type=dendropy.DnaCharacterMatrix,
distinct_state_alphabets=False,
distinct_taxa=True)
def testStandardRountTripSameTaxa(self):
c1 = datagen.reference_standard_matrix()
path = pathmap.named_output_path("char_rw_dna.nex")
c1.write_to_path(path, "nexus")
c2 = dendropy.StandardCharacterMatrix.get_from_path(
path, "nexus", taxon_set=c1.taxon_set)
self.assertDistinctButEqual(c1,
c2,
char_type=dendropy.StandardCharacterMatrix,
distinct_state_alphabets=None,
distinct_taxa=False)
def testStandardRountTripSameTaxa(self):
c1 = datagen.reference_standard_matrix()
path = pathmap.named_output_path("char_rw_dna.nex")
c1.write_to_path(path, "nexus")
c2 = dendropy.StandardCharacterMatrix.get_from_path(path, "nexus", taxon_set=c1.taxon_set)
self.assertDistinctButEqual(
c1,
c2,
char_type=dendropy.StandardCharacterMatrix,
distinct_state_alphabets=None,
distinct_taxa=False)
def testDnaRountTripDistinctTaxa(self):
c1 = datagen.reference_dna_matrix()
path = pathmap.named_output_path("char_rw_dna.nex")
c1.write_to_path(path, "nexus")
c2 = dendropy.DnaCharacterMatrix.get_from_path(path, "nexus")
self.assertDistinctButEqual(
c1,
c2,
char_type=dendropy.DnaCharacterMatrix,
distinct_state_alphabets=False,
distinct_taxa=True)
def testStandardRountTripDistinctTaxa(self):
c1 = datagen.reference_standard_matrix()
path = pathmap.named_output_path("char_rw_dna.nex")
c1.write_to_path(path, "nexus")
c2 = dendropy.StandardCharacterMatrix.get_from_stream(
open(path, "rU"), "nexus")
self.assertDistinctButEqual(c1,
c2,
char_type=dendropy.StandardCharacterMatrix,
distinct_state_alphabets=None,
distinct_taxa=True,
ignore_chartypes=True)
def testStandardRountTripDistinctTaxa(self):
c1 = datagen.reference_standard_matrix()
path = pathmap.named_output_path("char_rw_dna.nex")
c1.write_to_path(path, "nexus")
c2 = dendropy.StandardCharacterMatrix.get_from_stream(open(path, "rU"), "nexus")
self.assertDistinctButEqual(
c1,
c2,
char_type=dendropy.StandardCharacterMatrix,
distinct_state_alphabets=None,
distinct_taxa=True,
ignore_chartypes=True)
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")
def testReadingAndWritingCharMatrix(self):
dna1 = datagen.reference_dna_matrix()
output_path = pathmap.named_output_path(filename="roundtrip_test.fasta", suffix_timestamp=True)
dna1.write_to_path(output_path, 'fasta')
dna2 = dendropy.DnaCharacterMatrix.get_from_path(output_path, 'fasta')
self.assertDistinctButEqual(dna1, dna2)
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")
