def ucount(sitecol):
    """
    Used to count the number of unique bases in a site for snpstring.
    returns as a spstring with * and -
    """

    ## a list for only catgs
    catg = [i for i in sitecol if i in "CATG"]

    ## find sites that are ambigs
    where = [sitecol[sitecol == i] for i in "RSKYWM"]

    ## for each occurrence of RSKWYM add ambig resolution to catg
    for ambig in where:
        for _ in range(ambig.size):
            catg += list(AMBIGS[ambig[0]])

    ## if invariant return " "
    if len(set(catg)) < 2:
        return " "
    else:
        ## get second most common site
        second = Counter(catg).most_common()[1][1]
        if second > 1:
            return "*"
        else:
            return "-"
def ucount(sitecol):
    """
    Used to count the number of unique bases in a site for snpstring.
    returns as a spstring with * and -
    """

    ## a list for only catgs
    catg = [i for i in sitecol if i in "CATG"]

    ## find sites that are ambigs
    where = [sitecol[sitecol == i] for i in "RSKYWM"]

    ## for each occurrence of RSKWYM add ambig resolution to catg
    for ambig in where:
        for _ in range(ambig.size):
            catg += list(AMBIGS[ambig[0]])

    ## if invariant return " "
    if len(set(catg)) < 2:
        return " "
    else:
        ## get second most common site
        second = Counter(catg).most_common()[1][1]
        if second > 1:
            return "*"
        else:
            return "-"
def ucount ( sitecol ) : ## a list for only catgs catg = [ i for i in sitecol if i in "CATG" ] ## find sites that are ambigs where = [ sitecol [ sitecol == i ] for i in "RSKYWM" ] ## for each occurrence of RSKWYM add ambig resolution to catg for ambig in where : for _ in range ( ambig . size ) : catg += list ( AMBIGS [ ambig [ 0 ] ] ) ## if invariant return " " if len ( set ( catg ) ) < 2 : return " " else : ## get second most common site second = Counter ( catg ) . most_common ( ) [ 1 ] [ 1 ] if second > 1 : return "*" else : return "-"
Used to count the number of unique bases in a site for snpstring.
    returns as a spstring with * and -
Used to count the number of unique bases in a site for snpstring . returns as a spstring with * and -