trapes.py 文件源码

def getUnDictRatio(bamF, start, end, tcr, unDict):
    unMappedCount = 0
    usedArr = []
    mappedFile = pysam.AlignmentFile(bamF,"rb")
    readsIter = mappedFile.fetch(tcr, start, end)
    for read in readsIter:
        if read.is_read1 :
            newName =  read.query_name + '_1'
        else:
            newName = read.query_name + '_2'
        if newName not in usedArr:
            usedArr.append(newName)
            if newName in unDict:
                unMappedCount += 1
    mappedFile.close()
    return (float(float(unMappedCount)/len(unDict)), unMappedCount)