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# Copyright 2013 by Zheng Ruan (zruan1991@gmail.com).
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code for Codon Alphabet.
CodonAlphabet class is inherited from Alphabet class. It is an
alphabet for CodonSeq class.
"""
import copy
try:
from itertools import izip
except ImportError:
izip = zip
from Bio.Alphabet import IUPAC, Gapped, HasStopCodon, Alphabet
from Bio.Data.CodonTable import generic_by_id
default_codon_table = copy.deepcopy(generic_by_id[1])
def get_codon_alphabet(alphabet, gap="-", stop="*"):
"""Gets alignment alphabet for codon alignment.
Only nucleotide alphabet is accepted. Raise an error when the type of
alphabet is incompatible.
"""
from Bio.Alphabet import NucleotideAlphabet
if isinstance(alphabet, NucleotideAlphabet):
alpha = alphabet
if gap:
alpha = Gapped(alpha, gap_char=gap)
if stop:
alpha = HasStopCodon(alpha, stop_symbol=stop)
else:
raise TypeError("Only Nuclteotide Alphabet is accepted!")
return alpha
default_alphabet = get_codon_alphabet(IUPAC.unambiguous_dna)
class CodonAlphabet(Alphabet):
"""Generic Codon Alphabet with a size of three"""
size = 3
letters = None
name = ''
def __repr__(self):
return "%s(%s)" % (self.__class__.__name__, self.names[0])
def get_codon_alphabet(codon_table, gap_char="-"):
letters = list(codon_table.forward_table.keys())
letters.extend(codon_table.stop_codons)
letters.extend(codon_table.start_codons)
if gap_char:
letters.append(gap_char * 3)
generic_codon_alphabet = CodonAlphabet()
generic_codon_alphabet.letters = letters
generic_codon_alphabet.gap_char = '-'
generic_codon_alphabet.names = codon_table.names
return generic_codon_alphabet
default_codon_alphabet = get_codon_alphabet(default_codon_table)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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