code: def scaffold_hits(searches, fasta, max_hits):
      
      # initialize
      ## scaffolds[scaffold] = # ORFs
      scaffolds = {}
      for seq in parse_fasta(fasta):
          scaffold = seq[0].split()[0].split('>', 1)[1].rsplit('_', 1)[0]
          if scaffold not in scaffolds:
              scaffolds[scaffold] = 0
          scaffolds[scaffold] += 1
      s2rp = {s: {r[0]: []
          for r in searches}
          for s in scaffolds}
      # get hits from blast
      for search in searches:
          rp, blast = search
          hits = [i for i in numblast(open(blast), max_hits, evalue_thresh, bit_thresh)]
          for hit in hits:
              s = hit[0].split()[0].rsplit('_', 1)[0]
              hit[10], hit[11] = float(hit[10]), float(hit[11])
              s2rp[s][rp].append(hit)
      return scaffolds, s2rp
docs: get hits from each search against each RP
      scaffolds[scaffold] = # ORfs
      s2rp[scaffold] = {rp:[hits]}