read_scanner.py 文件源码

def kmer_freq ( mode, ref_str, strand, opts ):
    ref_str = ref_str.upper()
    if strand==1:
        ref_str = ref_str[::-1]
    k = opts.comp_kmer
    kmers = []
    for seq in product("ATGC",repeat=k):
        kmers.append( "".join(seq) )

    kmer_counts = Counter()
    for j in range( len(ref_str)-(k-1) ):
        motif    = ref_str[j:j+k]
        kmer_counts[motif] += 1

    # Combine forward and reverse complement motifs into one count
    combined_kmer = Counter()
    for kmer in kmers:
        kmer_rc = motif_tools.rev_comp_motif(kmer)
        if not combined_kmer.get(kmer_rc):
            combined_kmer[kmer] = kmer_counts[kmer] + kmer_counts[kmer_rc] + 1

    return combined_kmer