manipulateSeq.py 文件源码

def align_one(ssw, qProfile, rNum, nRLen, nOpen, nExt, nFlag, nMaskLen):
    """
    this function calculate the score and other results from the alignment
    """
    res = ssw.ssw_align(qProfile, rNum, ct.c_int32(nRLen), nOpen, nExt, nFlag, 0, 0, int(nMaskLen))
    nScore = res.contents.nScore
    nScore2 = res.contents.nScore2
    nRefBeg = res.contents.nRefBeg
    nRefEnd = res.contents.nRefEnd
    nQryBeg = res.contents.nQryBeg
    nQryEnd = res.contents.nQryEnd
    nRefEnd2 = res.contents.nRefEnd2
    lCigar = [res.contents.sCigar[idx] for idx in range(res.contents.nCigarLen)]
    nCigarLen = res.contents.nCigarLen
    ssw.align_destroy(res)
    return nScore, nScore2, nRefBeg, nRefEnd, nQryBeg, nQryEnd, nRefEnd2, nCigarLen, lCigar