comparison NanocomporeDB_process.py @ 3:b833eff63b10 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit c2985b5c91a932e175cbfaf9b54a76e23beff9e9"

2:25abc2c72ff9

    parser.add_argument('--pvalue-types', type=str,
                        default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue',
                        help='path to the annotations')
    parser.add_argument('--bedgraph', action="store_true",
                        help='write output in BEDGRAPH format instead of BED')
    parser.add_argument('--pvalue-threshold', default=1.0,
                        help='Maximum reported p-value.')
    parser.add_argument('--out-dir', default="./", type=is_valid_directory,
                        help='path the plotting output directory.')

    args = parser.parse_args()

    db = SampCompDB(args.db_path, fasta_fn=args.ref_fasta,
                    bed_fn=args.annotation_bed)
    print(db)
    print("DB read ids:", db.ref_id_list)

    if args.annotation_bed:
        for pt in args.pvalue_types.split(','):
            print("bedgraph output for p-value type:", pt)
            db.save_to_bed(output_fn='{}/{}.bedgraph'.format(args.out_dir, pt),
                           pvalue_field=pt, pvalue_thr=args.pvalue_threshold,
                           bedgraph=args.bedgraph)

3:b833eff63b10

    parser.add_argument('--pvalue-types', type=str,
                        default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue',
                        help='path to the annotations')
    parser.add_argument('--bedgraph', action="store_true",
                        help='write output in BEDGRAPH format instead of BED')
    parser.add_argument('--pvalue-threshold', type=float, default=1.0,
                        help='Maximum reported p-value.')
    parser.add_argument('--out-dir', default="./", type=is_valid_directory,
                        help='path the plotting output directory.')

    args = parser.parse_args()

    db = SampCompDB(args.db_path, fasta_fn=args.ref_fasta,
                    bed_fn=args.annotation_bed)
    print(db)
    print("DB read ids:", db.ref_id_list)

    if args.bedgraph:
        file_ext = 'bedgraph'
    else:
        file_ext = 'bed'

    if args.annotation_bed:
        for pt in args.pvalue_types.split(','):
            out_path = '{}/{}.{}'.format(args.out_dir, pt, file_ext)
            print("%s output for p-value type:" % out_path, pt)
            db.save_to_bed(output_fn=out_path,
                           pvalue_field=pt, pvalue_thr=args.pvalue_threshold,
                           bedgraph=args.bedgraph)