ipyrad/assemble/util.py
def fullcomp(seq):
    """ returns complement of sequence including ambiguity characters,
    and saves lower case info for multiple hetero sequences"""
    ## this is surely not the most efficient...
    seq = seq.replace("A", 'u')\
             .replace('T', 'v')\
             .replace('C', 'p')\
             .replace('G', 'z')\
             .replace('u', 'T')\
             .replace('v', 'A')\
             .replace('p', 'G')\
             .replace('z', 'C')

    ## No complement for S & W b/c complements are S & W, respectively
    seq = seq.replace('R', 'u')\
             .replace('K', 'v')\
             .replace('Y', 'b')\
             .replace('M', 'o')\
             .replace('u', 'Y')\
             .replace('v', 'M')\
             .replace('b', 'R')\
             .replace('o', 'K')

    seq = seq.replace('r', 'u')\
             .replace('k', 'v')\
             .replace('y', 'b')\
             .replace('m', 'o')\
             .replace('u', 'y')\
             .replace('v', 'm')\
             .replace('b', 'r')\
             .replace('o', 'k')
    return seq
def fullcomp(seq):
    """ returns complement of sequence including ambiguity characters,
    and saves lower case info for multiple hetero sequences"""
    ## this is surely not the most efficient...
    seq = seq.replace("A", 'u')\
             .replace('T', 'v')\
             .replace('C', 'p')\
             .replace('G', 'z')\
             .replace('u', 'T')\
             .replace('v', 'A')\
             .replace('p', 'G')\
             .replace('z', 'C')

    ## No complement for S & W b/c complements are S & W, respectively
    seq = seq.replace('R', 'u')\
             .replace('K', 'v')\
             .replace('Y', 'b')\
             .replace('M', 'o')\
             .replace('u', 'Y')\
             .replace('v', 'M')\
             .replace('b', 'R')\
             .replace('o', 'K')

    seq = seq.replace('r', 'u')\
             .replace('k', 'v')\
             .replace('y', 'b')\
             .replace('m', 'o')\
             .replace('u', 'y')\
             .replace('v', 'm')\
             .replace('b', 'r')\
             .replace('o', 'k')
    return seq
returns complement of sequence including ambiguity characters,
    and saves lower case info for multiple hetero sequences