utils.py 文件源码

def fastq_info(path):
    """ Found some info about how to ignore warnings in code blocks here:
      - http://stackoverflow.com/questions/14463277/how-to-disable-python-warnings
    """
    numBases = 0
    numReads = 0
    readLengths = Counter()
    GCTot = 0
    with warnings.catch_warnings():
        warnings.simplefilter("ignore")
        handle = gzip.open(path, "rt")
        for record in SeqIO.parse(handle, "fastq"):
            numBases += len(record)
            numReads += 1
            readLengths[len(record)] += 1
            GCTot += sum(record.seq.count(x) for x in ['G', 'C', 'g', 'c', 'S', 's'])
        handle.close()
    GCPer = (GCTot/numBases)
    avgReadLen = (sum(value*count for value,count in readLengths.items())/numReads)
    return {"numBases": numBases,
            "numReads": numReads,
            "numGCBases": GCTot,
            "portionGC": GCPer,
            "avgReadLen": avgReadLen}