1 import string, re
2
3
4
5
7 size = None
8 letters = None
9
11 return self.__class__.__name__ + "()"
12
14 return isinstance(other, self.__class__)
15
16 generic_alphabet = Alphabet()
17
21
22 single_letter_alphabet = SingleLetterAlphabet()
23
24
25
28
29 generic_protein = ProteinAlphabet()
30
31
34
35 generic_nucleotide = NucleotideAlphabet()
36
39
40 generic_dna = DNAAlphabet()
41
42
43
44
47
48 generic_rna = RNAAlphabet()
49
50
51
52
53
56
58 size = 3
59 letters = [
60 "Ala", "Asx", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile",
61 "Lys", "Leu", "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr",
62 "Sec", "Val", "Trp", "Xaa", "Tyr", "Glx",
63 ]
64
65
66
67
68
70 - def __init__(self, alphabet, new_letters):
78 if key[:2] == "__" and key[-2:] == "__":
79 raise AttributeError(key)
80 return getattr(self.alphabet, key)
81
83 return "%s(%r, %r)" % (self.__class__.__name__, self.alphabet,
84 self.new_letters)
85
88
90 - def __init__(self, alphabet, gap_char = "-"):
93
97
99 - def __init__(self, alphabet, stop_symbol = "*"):
102
104 x = cmp(self.alphabet, other.alphabet)
105 if x == 0:
106 return cmp(self.stop_symbol, other.stop_symbol)
107 return x
108
112