gistfile1.txt

#!/usr/bin/env python
import re
import sys

e = 0
w = 0

def exxx(m):
    global e
    e += 1
    return '<span id="E%03d">%s</span>' % (e, m.group(1))

def wxxx(m):
    global w
    w += 1
    return '<span id="W%03d">%s</span>' % (w, m.group(1))

with open('index.html', 'r') as fh:
    for line in fh:
        line = re.sub(r'''(MUST NOT|MUST)''', exxx, line)
        line = re.sub(r'''(SHOULD NOT|SHOULD)''', wxxx, line)
        sys.stdout.write(line)