dc719925f9202a1248d2510aa7aa7e3b648f82cc,bin/basenji_scent.py,,main,#,26

Before Change

    targets_t = []
    for sample in target_wigs:
        wig_file = target_wigs[sample]
        print("  %s" % wig_file)
        sys.stdout.flush()

        // initialize new row
        targets_t.append([])

        // open wig
        wig_in = pyBigWig.open(wig_file)

        for chrom in chrom_samples:
            for pos in chrom_samples[chrom]:
                try:
                    pos_val = wig_in.values(chrom, pos, pos+1)[0]
                except:
                    print(chrom,pos)
                    exit(1)
                targets_t[-1].append(pos_val)

    // convert and transpose
    targets = np.array(targets_t).T

After Change

    t0 = time.time()

    p = multiprocessing.Pool(options.processes)
    targets_t = p.starmap(bigwig_read, [(wig_file, chrom_samples) for wig_file in target_wigs.values()])

    // convert and transpose
    targets = np.array(targets_t).T

Instances