Python reference_standard_matrix Examples

Example #1

File: test_dataobject_dataset.py Project: emilhaegglund/wgfast

 def testSimpleCopyStandardMatrix(self):
     char_matrix = datagen.reference_standard_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)

Example #2

File: test_dataobject_dataset.py Project: jjhoyt/gengis

 def testSimpleCopyStandardMatrix(self):
     char_matrix = datagen.reference_standard_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)

Example #3

File: test_dataobject_char_array.py Project: nesnidal/DendroPy

 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)

Example #4

File: test_dataobject_char_array.py Project: jjhoyt/gengis

 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)

Example #5

 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)

Example #6

File: test_dataobject_char_array.py Project: BioinformaticsArchive/DendroPy

 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)

Example #7

 def setUp(self):
     self.char_matrix1 = datagen.reference_standard_matrix()

Example #8

File: test_ape.py Project: emilhaegglund/wgfast

 def setUp(self):
     self.trees = datagen.reference_tree_list()
     self.dna_chars = datagen.reference_dna_matrix()
     self.std_chars = datagen.reference_standard_matrix()

Example #9

File: test_ape.py Project: jjhoyt/gengis

 def setUp(self):
     self.trees = datagen.reference_tree_list()
     self.dna_chars = datagen.reference_dna_matrix()
     self.std_chars = datagen.reference_standard_matrix()

Example #10

File: test_dataobject_char_array.py Project: BioinformaticsArchive/DendroPy

 def setUp(self):
     self.char_matrix1 = datagen.reference_standard_matrix()

Example #11

File: test_biopython.py Project: BioinformaticsArchive/DendroPy

 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)

Example #12

File: test_biopython.py Project: nesnidal/DendroPy

 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)