process.py

import sys, os.path

settings_file = sys.argv[1]
id_list_file  = sys.argv[2]

f = open(settings_file)
settings = f.read()
f.close()
f = open(id_list_file)
ids = f.read()
f.close()

# Get every line, split by new lines, otherwise unmodified
settings = [x for x in settings.split('\n')]
# Get every id, split by whitespace (newlines, tabs, spaces, etc.)
ids = ids.split()

mode = 0
for i, line in enumerate(settings):
    # Only pay attention to lines with content
    if line.strip():
        if (mode == 0) and line.startswith('['):
            # New block, see if id matches
            if line.strip('[]') in ids:
                # Block matches, start commenting
                settings[i] = ';' + settings[i]
                mode = 1
        elif (mode == 1):
            settings[i] = ';' + settings[i]
    else:
        # No content = end of block = reset mode
        mode = 0

fname, fext = os.path.splitext(settings_file)
f = open(fname + '_out' + fext, 'w')
f.write('\n'.join(settings))
f.close()