def to_nuc(self, table='standard', rna=False):
from ochre.Misc import tTables
tab = tTables(table)
try:
rseq = ''.join([tab[i][0] for i in self.seq])
except KeyError:
raise KeyError('Amino acid not found in table.')
if rna:
return Seq(rseq.replace('T', 'U'), seq_type='RNA')
else:
return Seq(rseq, seq_type='DNA')
def to_pep(self, table='standard'):
from ochre.Misc import tTables
tab = tTables(table)
flatten = lambda l: [item for sublist in l for item in sublist]
rtab = dict(flatten([zip(tab[i], len(tab[i]) * [i]) for i in tab]))
if self._is_rna():
rtab = dict([(i.replace('T', 'U'), rtab[i]) for i in rtab])
rseq = ''.join(rtab.get(cdn, 'X') for cdn \
in self.slid_win(3, overlapping=False) if len(cdn) == 3)
return Seq(rseq, seq_type='PROTEIN')
