demultiplex.py 文件源码

def run(parser, args):
    tmpdir = tempfile.mkdtemp(dir='.')

    cmd = ("porechop --verbosity 2 --untrimmed -i \"%s\" -b %s --barcode_threshold 80 --threads %s --check_reads 10000 --barcode_diff 5 --require_two_barcodes > %s.demultiplexreport.txt" % (args.fasta, tmpdir, args.threads, args.fasta))
    print >>sys.stderr, cmd
    os.system(cmd)

    a, b = os.path.split(args.fasta)
    prefix, ext = os.path.splitext(b)

    for fn in os.listdir(tmpdir):
        newfn = "%s-%s" % (prefix, os.path.basename(fn))
        shutil.move(tmpdir + '/' + fn, newfn)

        os.system("gunzip -f %s" % (newfn,))

    if not args.no_remove_directory:
        os.rmdir(tmpdir)