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178 def lexicographic(alphabet): 179 for n in count(): 180 for e in product(alphabet, repeat = n): 181 yield e
141 def __iter__(self): 142 for i in range(len(self)): 143 yield self._flip[i]
32 def _generateAlphabet(needle, haystack): 33 alphabet = {} 34 for letter in haystack: 35 if letter not in alphabet: 36 letterPositionInNeedle = 0 37 for symbol in needle: 38 letterPositionInNeedle = letterPositionInNeedle << 1 39 letterPositionInNeedle |= int(letter != symbol) 40 alphabet[letter] = letterPositionInNeedle 41 return alphabet
639 def _force_alphabet(record_iterator, alphabet): 640 """Iterate over records, over-riding the alphabet (PRIVATE).""" 641 # Assume the alphabet argument has been pre-validated 642 given_base_class = _get_base_alphabet(alphabet).__class__ 643 for record in record_iterator: 644 if isinstance(_get_base_alphabet(record.seq.alphabet), given_base_class): 645 record.seq.alphabet = alphabet 646 yield record 647 else: 648 raise ValueError( 649 "Specified alphabet %r clashes with " 650 "that determined from the file, %r" % (alphabet, record.seq.alphabet) 651 )