Python SequenceDataset示例

示例#1

 def test1000T(self):
     sd = SequenceDataset()
     fp = data_source_path('1000T.fasta')
     sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')
     fp = data_source_path('1000T.tree')
     tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU"))
     self.assertEqual(len(tree_list), 1)

示例#2

文件： test_alignment.py 项目： SagesWang/pasta

 def test1000T(self):
     sd = SequenceDataset()
     fp = data_source_path('1000T.fasta')
     sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')
     fp = data_source_path('1000T.tree')
     tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU"))
     self.assertEqual(len(tree_list), 1)

示例#3

 def testCentroidEdge(self):
     sd = SequenceDataset()
     fp = data_source_path('100T.fasta')
     sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')
     fp = data_source_path('100T.tree')
     tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU"))
     self.assertEqual(len(tree_list), 1)
     t = PhylogeneticTree(tree_list[0])
     self._do_test_centroid(t)

示例#4

文件： test_decomp.py 项目： SagesWang/pasta

 def testCentroidEdge(self):
     sd = SequenceDataset()
     fp = data_source_path('100T.fasta')
     sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')
     fp = data_source_path('100T.tree')
     tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU"))
     self.assertEqual(len(tree_list), 1)
     t = PhylogeneticTree(tree_list[0])
     self._do_test_centroid(t)

示例#5

 def testDNAFasta(self):
     sd = SequenceDataset()
     fp = data_source_path('anolis.fasta')
     sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')

示例#6

文件： test_alignment.py 项目： SagesWang/pasta

 def testDNAFasta(self):
     sd = SequenceDataset()
     fp = data_source_path('anolis.fasta')
     sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')