embed some prints in your code to see why the if part doesn't resolve to true. prpps = primer_record.primer_processed_seq rps = record.processed_seq rrs = record.reverse_seq print prpps print rps print rrs print 'first condition evaluates to ', prpps in rps print 'second condition evaluates to ', prpps in rrs print 'ORing conditions leads to ', prpps in rps or prpps in rrs
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