nanoQC.py 文件源码

def main():
    args = get_args()
    logging.basicConfig(
        format='%(asctime)s %(message)s',
        filename=os.path.join(args.outdir, "NanoQC.log"),
        level=logging.INFO)
    logging.info("NanoQC started.")
    sizeRange = length_histogram(
        fqin=gzip.open(args.fastq, 'rt'),
        name=os.path.join(args.outdir, "SequenceLengthDistribution.png"))
    fq = get_bin(gzip.open(args.fastq, 'rt'), sizeRange)
    logging.info("Using {} reads for plotting".format(len(fq)))
    fqbin = [dat[0] for dat in fq]
    qualbin = [dat[1] for dat in fq]
    logging.info("Creating plots...")
    per_base_sequence_content_and_quality(fqbin, qualbin, args.outdir, args.format)
    logging.info("per base sequence content and quality completed.")
    logging.info("Finished!")