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

Before Change

        // 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

    // shuffle
    np.random.shuffle(targets)

After Change

    parser = OptionParser(usage)
    parser.add_option("-g", dest="gaps_file", help="Genome assebmly gaps BED [Default: %default]")
    parser.add_option("-m", dest="params_file", help="Model parameters")
    parser.add_option("-p", dest="processes", default=1, type="int", help="Number parallel processes to load data [Default: %default]")
    parser.add_option("-s", dest="sample", type="int", default=1000, help="Genomic positions to sample for training data [Default: %default]")
    parser.add_option("-v", dest="valid_pct", type="float", default=0.1, help="Proportion of the data for validation [Default: %default]")
    (options,args) = parser.parse_args()

Instances