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src/b/i/biopython-HEAD/Bio/CodonAlign/CodonAlignment.py biopython(Download)
def get_dn_ds_matrix(self, method="NG86"): """Available methods include NG86, LWL85, YN00 and ML. """ from Bio.Phylo.TreeConstruction import _DistanceMatrix as DM names = [i.id for i in self._records]
dn_matrix[i].append(0.0) ds_matrix[i].append(0.0) dn_dm = DM(names, matrix=dn_matrix) ds_dm = DM(names, matrix=ds_matrix) return dn_dm, ds_dm
src/b/i/biopython-HEAD/Tests/test_TreeConstruction.py biopython(Download)
from Bio.Phylo import Consensus from Bio.Phylo.TreeConstruction import _Matrix from Bio.Phylo.TreeConstruction import _DistanceMatrix from Bio.Phylo.TreeConstruction import DistanceCalculator from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
def test_good_construction(self): dm = _DistanceMatrix(self.names, self.matrix) self.assertTrue(isinstance(dm, TreeConstruction._DistanceMatrix)) self.assertEqual(dm.names[0], 'Alpha') self.assertEqual(dm.matrix[2][1], 3)
def test_good_manipulation(self): dm = _DistanceMatrix(self.names, self.matrix) # getitem self.assertEqual(dm[1], [1, 0, 3, 5]) self.assertEqual(dm[2, 1], 3)
def test_bad_manipulation(self): dm = _DistanceMatrix(self.names, self.matrix) #getitem self.assertRaises(ValueError, dm.__getitem__, 'A') self.assertRaises(ValueError, dm.__getitem__, ('Alpha', 'A'))