controls.py 文件源码

def chunk_control_matrices( self, control_ipds_fn, control_ipds_N_fn, control_kmers_fn ):
        """

        """
        kmers       = np.atleast_1d(np.loadtxt(control_kmers_fn, dtype="str"))
        fns         = [control_ipds_fn, control_ipds_N_fn]
        n_chunks    = 99
        chunksize   = int(math.ceil(float( len(kmers)/n_chunks )))
        cols_chunks = list(chunks( range(len(kmers)), chunksize ))
        args        = []
        for i,cols_chunk in enumerate(cols_chunks):
            cut_CMDs = []
            for fn in fns:
                cut_cols = "%s-%s" % ((cols_chunk[0]+1), (cols_chunk[-1]+1))
                in_fn    = fn
                out_fn   = fn+".sub.%s" % i
                cut_CMD  = "cut -d$\'\\t\' -f%s %s > %s" % (cut_cols, in_fn, out_fn)
                cut_CMDs.append(cut_CMD)
            args.append( (i, cut_CMDs, kmers, cols_chunk, n_chunks, self.opts.min_motif_count) )

        results = mbin.launch_pool(self.opts.procs, process_contig_chunk, args)

        logging.info("Combining motifs from all chunks of control data...")
        not_found     = 0
        control_means = {}
        for i,result in enumerate(results):
            not_found += result[1]
            for motif in result[0].keys():
                control_means[motif] = result[0][motif]
        logging.info("Done.")

        return control_means,not_found