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import string, re
# This is used by sequences which contain a finite number of similar
# words.
class Alphabet:
size = None # no fixed size for words
letters = None # no fixed alphabet; implement as a list-like
# interface,
def __repr__(self):
return self.__class__.__name__ + "()"
def contains(self, other):
return isinstance(other, self.__class__)
generic_alphabet = Alphabet()
class SingleLetterAlphabet(Alphabet):
size = 1
letters = None # string of all letters in the alphabet
single_letter_alphabet = SingleLetterAlphabet()
########### Protein
class ProteinAlphabet(SingleLetterAlphabet):
pass
generic_protein = ProteinAlphabet()
########### DNA
class NucleotideAlphabet(SingleLetterAlphabet):
pass
generic_nucleotide = NucleotideAlphabet()
class DNAAlphabet(NucleotideAlphabet):
pass
generic_dna = DNAAlphabet()
########### RNA
class RNAAlphabet(NucleotideAlphabet):
pass
generic_rna = RNAAlphabet()
########### Other per-sequence encodings
class SecondaryStructure(SingleLetterAlphabet):
letters = "HSTC"
class ThreeLetterProtein(Alphabet):
size = 3
letters = [
"Ala", "Asx", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile",
"Lys", "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr",
"Sec", "Val", "Trp", "Xaa", "Tyr", "Glx",
]
###### Non per-sequence modifications
# (These are Decorator classes)
class AlphabetEncoder:
def __init__(self, alphabet, new_letters):
self.alphabet = alphabet
self.new_letters = new_letters
if alphabet.letters is not None:
self.letters = alphabet.letters + new_letters
else:
self.letters = None
def __getattr__(self, key):
if key[:2] == "__" and key[-2:] == "__":
raise AttributeError(key)
return getattr(self.alphabet, key)
def __repr__(self):
return "%s(%r, %r)" % (self.__class__.__name__, self.alphabet,
self.new_letters)
def contains(self, other):
return 0
class Gapped(AlphabetEncoder):
gap_char = '-'
def __init__(self, alphabet, gap_char = gap_char):
AlphabetEncoder.__init__(self, alphabet, gap_char)
def contains(self, other):
return other.gap_char == self.gap_char and \
self.alphabet.contains(other.alphabet)
class HasStopCodon(AlphabetEncoder):
stop_symbol = "*"
def __init__(self, alphabet, stop_symbol = stop_symbol):
AlphabetEncoder.__init__(self, alphabet, stop_symbol)
def __cmp__(self, other):
x = cmp(self.alphabet, other.alphabet)
if x == 0:
return cmp(self.stop_symbol, other.stop_symbol)
return x
def contains(self, other):
return other.stop_symbol == self.stop_symbol and \
self.alphabet.contains(other.alphabet)
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