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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 interited from Alphabet class. It is an
alphabet for CodonSeq class.
"""
__docformat__ = "epytext en" # Don't just use plain text in epydoc API pages!
import copy
try:
from itertools import izip
except ImportError:
izip = zip
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC, Gapped, HasStopCodon, Alphabet, generic_dna
from Bio.Data.CodonTable import generic_by_id
default_codon_table = copy.deepcopy(generic_by_id[1])
def get_codon_alphabet(alphabet, gap="-", stop="*"):
"""function to get 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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