code: def parse_cutoff(motifs, cutoff, default=0.9):
      
      
      cutoffs = {}
      if os.path.isfile(str(cutoff)):
          for i,line in enumerate(open(cutoff)):
              if line != "Motif\tScore\tCutoff\n":
                  try:
                      motif,_,c = line.strip().split("\t")
                      c = float(c)
                      cutoffs[motif] = c
                  except Exception as e:
                      sys.stderr.write("Error parsing cutoff file, line {0}: {1}\n".format(e, i + 1))
                      sys.exit(1)
      else:
          for motif in motifs:
              cutoffs[motif.id] = float(cutoff)
      
      for motif in motifs:
          if not motif.id in cutoffs:
              sys.stderr.write("No cutoff found for {0}, using default {1}\n".format(motif.id, default))
              cutoffs[motif.id] = default
      return cutoffs
docs: Provide either a file with one cutoff per motif or a single cutoff
          returns a hash with motif id as key and cutoff as value