def ungap(self, gap=None):
if hasattr(self.alphabet, "gap_char"):
if not gap:
gap = self.alphabet.gap_char
elif gap != self.alphabet.gap_char:
raise ValueError("Gap %s does not match %s from alphabet"
% (repr(gap), repr(self.alphabet.alphabet.gap_char)))
alpha = _ungap(self.alphabet)
elif not gap:
raise ValueError("Gap character not given and not defined in "
"alphabet")
else:
alpha = self.alphabet # modify!
if len(gap) != 1 or not isinstance(gap, str):
raise ValueError("Unexpected gap character, %s" % repr(gap))
return CodonSeq(str(self._data).replace(gap, ""), alpha,
rf_table=self.rf_table)
def ungap(self, gap=None):
if hasattr(self.alphabet, "gap_char"):
if not gap:
gap = self.alphabet.gap_char
elif gap != self.alphabet.gap_char:
raise ValueError("Gap %s does not match %s from alphabet" %
(repr(gap), repr(self.alphabet.alphabet.gap_char)))
alpha = _ungap(self.alphabet)
elif not gap:
raise ValueError("Gap character not given and not defined in "
"alphabet")
else:
alpha = self.alphabet # modify!
if len(gap) != 1 or not isinstance(gap, str):
raise ValueError("Unexpected gap character, %s" % repr(gap))
return CodonSeq(str(self._data).replace(gap, ""), alpha,
rf_table=self.rf_table)