get hits from each search against each RP
    scaffolds[scaffold] = # ORfs
    s2rp[scaffold] = {rp:[hits]}

def scaffold_hits(searches, fasta, max_hits):
    """
    get hits from each search against each RP
    scaffolds[scaffold] = # ORfs
    s2rp[scaffold] = {rp:[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