def get_dn_ds_matrix(self, method="NG86", codon_table=default_codon_table):
"""Available methods include NG86, LWL85, YN00 and ML.
Argument:
- method - Available methods include NG86, LWL85, YN00 and ML.
- codon_table - Codon table to use for forward translation.
"""
from Bio.Phylo.TreeConstruction import _DistanceMatrix as DM
names = [i.id for i in self._records]
size = len(self._records)
dn_matrix = []
ds_matrix = []
for i in range(size):
dn_matrix.append([])
ds_matrix.append([])
for j in range(i + 1):
if i != j:
dn, ds = cal_dn_ds(self._records[i],
self._records[j],
method=method,
codon_table=codon_table)
dn_matrix[i].append(dn)
ds_matrix[i].append(ds)
else:
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
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]
size = len(self._records)
dn_matrix = []
ds_matrix = []
for i in range(size):
dn_matrix.append([])
ds_matrix.append([])
for j in range(i + 1):
if i != j:
dn, ds = cal_dn_ds(self._records[i], self._records[j],
method=method)
dn_matrix[i].append(dn)
ds_matrix[i].append(ds)
else:
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
