biglist = [['The', 'family'.....]['In', 'the']....]

clusters = [['the','in'...],['blood','gene'...]...].

test = biglist[0]

doc = []

for wo in test:
    for i, w in enumerate(clusters):
        for word in w:
            if wo in word:
                doc.append(i)
            else:
                doc.append('NAN')

print doc