controls.py 文件源码

def process_contig_chunk( args ):
    chunk_id        = args[0]
    cut_CMDs        = args[1]
    kmers           = args[2]
    cols_chunk      = args[3]
    n_chunks        = args[4]
    min_motif_count = args[5]
    logging.info("  - Control data: chunk %s/%s" % ((chunk_id+1), (n_chunks+1)))
    control_means = {}

    for cut_CMD in cut_CMDs:
        sts,stdOutErr = mbin.run_OS_command( cut_CMD )

    fns                = map(lambda x: x.split("> ")[-1], cut_CMDs)
    control_ipds_sub   = np.loadtxt(fns[0], dtype="float")
    control_ipds_N_sub = np.loadtxt(fns[1], dtype="int")
    # If there is only one row (read) for this contig, still treat as
    # a 2d matrix of many reads
    control_ipds_sub   = np.atleast_2d(control_ipds_sub)
    control_ipds_N_sub = np.atleast_2d(control_ipds_N_sub)

    not_found     = 0
    for j in range(len(cols_chunk)):
        motif = kmers[cols_chunk[j]]
        if np.sum(control_ipds_N_sub[:,j])>=min_motif_count:
            if np.sum(control_ipds_N_sub[:,j])>0:
                control_mean = np.dot(control_ipds_sub[:,j], control_ipds_N_sub[:,j]) / np.sum(control_ipds_N_sub[:,j])
            else:
                control_mean = 0
            control_means[motif] = control_mean
        else:
            not_found += 1

    return control_means,not_found