demultiplexON.py 文件源码

def generateSeqHandles(anIndexCfg):
    """
        The YAML config file to parse is like:

    handles:
        prefix: "TTAGTCTCCGACGGCAGGCTTCAAT"
        postfix: "ACGCACCCACCGGGACTCAG"
    indexes: [
        "ACAGTC",
        "TGATGC",
        "TCTCAG"
    ]

    There is a handle at one end of each sequence which is as follows:
    TTAGTCTCCGACGGCAGGCTTCAAT-ACAGTC-ACGCACCCACCGGGACTCAG
              prefix         -index -      postfix
    """
    forwardIdx= []     # the result array to collect handle sequence strings
    handlePrefix = anIndexCfg["handles"]["prefix"]
    handlePostfix = anIndexCfg["handles"]["postfix"]
    for index in anIndexCfg["indexes"]:
        forwardIdx.append(handlePrefix + index + handlePostfix)

    reverseIdx = []       # to collect reverse complements
    for handle in forwardIdx:
        seq = Seq(handle)
        rc = str(seq.reverse_complement())
        reverseIdx.append(rc)

    return (forwardIdx,reverseIdx)