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
def fullcomp ( seq ) : ## 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
returns complement of sequence including ambiguity characters and saves lower case info for multiple hetero sequences