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 testSimpleCopyDnaMatrix(self):
char_matrix = datagen.reference_dna_matrix()
ds1 = dendropy.DataSet(char_matrix)
self.assertEqual(len(ds1.char_matrices), 1)
self.assertIs(ds1.char_matrices[0], char_matrix)
ds2 = dendropy.DataSet(ds1)
self.assertDistinctButEqual(ds1, ds2)
def testSimpleCopyDnaMatrix(self):
char_matrix = datagen.reference_dna_matrix()
ds1 = dendropy.DataSet(char_matrix)
self.assertEqual(len(ds1.char_matrices), 1)
self.assertIs(ds1.char_matrices[0], char_matrix)
ds2 = dendropy.DataSet(ds1)
self.assertDistinctButEqual(ds1, ds2, ignore_chartypes=True)
def testDnaRountTripToStringDistinctTaxa(self):
c1 = datagen.reference_dna_matrix()
s1 = c1.as_string(schema="nexus")
c2 = dendropy.DnaCharacterMatrix.get_from_string(s1, "nexus")
self.assertDistinctButEqual(c1,
c2,
char_type=dendropy.DnaCharacterMatrix,
distinct_state_alphabets=False,
distinct_taxa=True)
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 testDnaRountTripToStringDistinctTaxa(self):
c1 = datagen.reference_dna_matrix()
s1 = c1.as_string(schema="nexus")
c2 = dendropy.DnaCharacterMatrix.get_from_string(s1, "nexus")
self.assertDistinctButEqual(
c1,
c2,
char_type=dendropy.DnaCharacterMatrix,
distinct_state_alphabets=False,
distinct_taxa=True)
def testDnaRountTripSameTaxa(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", taxon_set=c1.taxon_set)
self.assertDistinctButEqual(
c1,
c2,
char_type=dendropy.DnaCharacterMatrix,
distinct_state_alphabets=False,
distinct_taxa=False)
def test_dna_round_trip(self):
ds1 = datagen.reference_dna_matrix()
rw_kwargs = {
'data_type': 'dna',
'underscores_to_spaces': True,
'spaces_to_underscores': True
}
self.roundTripData(ds1,
'phylip',
writer_kwargs=rw_kwargs,
reader_kwargs=rw_kwargs)
def testReferenceDnaMatrix(self):
char_matrix = datagen.reference_dna_matrix()
taxon_set = char_matrix.taxon_set
dna_dict = datagen.reference_dna_dict()
self.assertEqual(len(char_matrix), 33)
self.assertIs(char_matrix.default_state_alphabet, dendropy.DNA_STATE_ALPHABET)
for tax_label, tax_seq_symbols in dna_dict.items():
taxon = taxon_set.require_taxon(label=tax_label)
self.assertIn(taxon, char_matrix)
seq_vec = char_matrix[taxon]
self.assertEqual(len(seq_vec), len(tax_seq_symbols))
for si, s1 in enumerate(tax_seq_symbols):
state = seq_vec[si].value
self.assertEqual(state.symbol, s1)
self.assertEqual(seq_vec.symbols_as_string(), tax_seq_symbols)
def testReferenceDnaMatrix(self):
char_matrix = datagen.reference_dna_matrix()
taxon_set = char_matrix.taxon_set
dna_dict = datagen.reference_dna_dict()
self.assertEqual(len(char_matrix), 33)
self.assertIs(char_matrix.default_state_alphabet,
dendropy.DNA_STATE_ALPHABET)
for tax_label, tax_seq_symbols in dna_dict.items():
taxon = taxon_set.require_taxon(label=tax_label)
self.assertIn(taxon, char_matrix)
seq_vec = char_matrix[taxon]
self.assertEqual(len(seq_vec), len(tax_seq_symbols))
for si, s1 in enumerate(tax_seq_symbols):
state = seq_vec[si].value
self.assertEqual(state.symbol, s1)
self.assertEqual(seq_vec.symbols_as_string(), tax_seq_symbols)
def setUp(self):
self.trees = datagen.reference_tree_list()
self.dna_chars = datagen.reference_dna_matrix()
self.std_chars = datagen.reference_standard_matrix()
def testReadingAndWritingDataSet(self):
ds1 = dendropy.DataSet(datagen.reference_dna_matrix())
dataset = self.roundTripDataSetTest(ds1, "fasta", reader_kwargs={'data_type': 'dna'})
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.trees = datagen.reference_tree_list()
self.dna_chars = datagen.reference_dna_matrix()
self.std_chars = datagen.reference_standard_matrix()
def setUp(self):
self.char_matrix1 = datagen.reference_dna_matrix()
def setUp(self):
self.taxon_set = datagen.reference_taxon_set()
self.dna_matrix = datagen.reference_dna_matrix(self.taxon_set)
self.std_matrix = datagen.reference_standard_matrix(self.taxon_set)
self.cont_matrix = datagen.reference_continuous_matrix(self.taxon_set)
def setUp(self):
self.taxon_set = datagen.reference_taxon_set()
self.dna_matrix = datagen.reference_dna_matrix(self.taxon_set)
self.std_matrix = datagen.reference_standard_matrix(self.taxon_set)
self.cont_matrix = datagen.reference_continuous_matrix(
self.taxon_set)
def test_dna_round_trip(self):
ds1 = datagen.reference_dna_matrix()
rw_kwargs = {'data_type': 'dna', 'underscores_to_spaces': True, 'spaces_to_underscores': True}
self.roundTripData(ds1, 'phylip', writer_kwargs=rw_kwargs, reader_kwargs=rw_kwargs)
def setUp(self):
self.char_matrix1 = datagen.reference_dna_matrix()
def testReadingAndWritingDataSet(self):
ds1 = dendropy.DataSet(datagen.reference_dna_matrix())
dataset = self.roundTripDataSetTest(ds1, "fasta", reader_kwargs={'data_type': 'dna'})
