Пример #1
0
def assemble_paired_end_reads(args, velvet_optimiser, indiv, read, interleaved_dir):
    assert is_dir(interleaved_dir), IOError("Directory {} containing interleaved reads does not exist".format(interleaved_dir))
    singletons = os.path.join(
            interleaved_dir,
            "{0}{1}".format(indiv, '-READ-singleton.fastq.gz')
        )
    interleaved = os.path.join(
            interleaved_dir,
            "{0}{1}".format(indiv, '-READ1and2-interleaved.fastq.gz')
        )
    for f in [singletons, interleaved]:
        assert os.path.isfile(f), IOError("Missing sequence file(s): {0}".format(f))
    assembly_dir = os.path.join(args.output, indiv, 'assembly')
    mkdir_p(assembly_dir)
    os.chdir(assembly_dir)
    velveth = "-fastq.gz -shortPaired {} -short {}".format(singletons, interleaved)
    cmd = [velvet_optimiser,
            "-s", args.s,
            "-e", args.e,
            "-c", "'ncon'",
            "-t", args.t,
            "-a",
            "-f", velveth
        ]
    stdout, stderr = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
    return stdout, stderr, assembly_dir