comparison summarize_alignment.py @ 2:5c8dfc4d9d68 draft

planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty

1:f2a7aaf93a1d

    parser.add_argument("--summary_output_filename", help="Path to summary output file")
    parser.add_argument("--variant_list_outputs", nargs="+")
    parser.add_argument("--datasets", nargs="+")
    args = parser.parse_args()

    summary_output = open(args.summary_output_filename, "w")
    for i, json_filename in enumerate(args.datasets):
        alignment_summary = json.load(open(json_filename))
        mismatch_list = ";".join(
            [

        )
        print(
            alignment_summary["sample_name"],
            alignment_summary["best_reference"],
            alignment_summary["mismatches"],
            round(alignment_summary["quality"], 2),
            mismatch_list,
            sep="\t",
            file=summary_output,
        )

2:5c8dfc4d9d68

    parser.add_argument("--summary_output_filename", help="Path to summary output file")
    parser.add_argument("--variant_list_outputs", nargs="+")
    parser.add_argument("--datasets", nargs="+")
    args = parser.parse_args()

    galaxy_metadata = {}
    summary_output = open(args.summary_output_filename, "w")
    for i, json_filename in enumerate(args.datasets):
        alignment_summary = json.load(open(json_filename))
        mismatch_list = ";".join(
            [

        )
        print(
            alignment_summary["sample_name"],
            alignment_summary["best_reference"],
            alignment_summary["mismatches"],
            alignment_summary["perc_mismatches"],
            round(alignment_summary["quality"], 2),
            mismatch_list,
            sep="\t",
            file=summary_output,
        )