Features missing from Python's string/list types that are handy for bio-informatics

bioinfo_funcs.py

"Functions missing from Python's string/list types that are handy for bio-informatics."

def codonise(seq):
    '''Returns a list of codons, not including trailing 1/2n.
    To get codons starting from letter X, pass seq[X:].'''
    mylist = []
    for i in range(0, len(seq), 3):
        this_codon = seq[i:i+3]
        # This bit ensures that only whole codons,
        # not trailing bits, are added:
        if len(this_codon) is 3:
            mylist.append( this_codon )
    return mylist

def allindices(string, substring):
    'Returns a list of ALL indices of a substring, not just first.'
    listindex = []
    i = string.find(substring)
    while i >= 0: # Because find returns -1 when it finds nothing.
        listindex.append(i)
        i = string.find(substring, i + 1)
    return listindex