trapes.py 文件源码

def writeFailedReconstructions(outF, chain, writtenArr, output, idNameDict, fastaDict):
    recF = output + '.reconstructed.junctions.' + chain + '.fa'
    if os.path.isfile(recF):
        f = open(recF, 'rU')
        segDict = dict()
        for tcrRecord in SeqIO.parse(f, 'fasta'):
            tcrSeq = str(tcrRecord.seq)
            if tcrSeq.find('NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN') != -1:
                status = 'Failed reconstruction - reached maximum number of iterations'
                segDict = addSegmentsToDict(segDict, status, writtenArr, tcrRecord, idNameDict, fastaDict)
            elif tcrSeq.find('NNNN') != -1:
                status = 'Failed reconstruction - V and J segment do not overlap'
                segDict = addSegmentsToDict(segDict, status, writtenArr, tcrRecord, idNameDict, fastaDict)
        f.close()
        if len(segDict) > 0:
            writeSegDict(segDict, outF, chain)