comparison run_lastz_tarball.py @ 16:79182c2a8c80 draft default tip

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit e03d88240ee3894a2bb7bf2f196d9215cb8e0621

15:f6090d2a5722

                format_name = f.readline()
                format_name = format_name.rstrip("\n")
        except FileNotFoundError:
            sys.exit(f"ERROR: input tarball missing galaxy/format.txt: {self.pathname}")

        if format_name in ["axt", "bam", "maf"]:
            self.format_name = format_name
        elif format_name == "differences":
            self.format_name = "interval"


class TarRunner:
    def __init__(
        self,

                    found_falures = True

            while not output_queue.empty():
                run_time = output_queue.get()
                run_times.append(run_time)

            if found_falures:
                sys.exit("lastz command failed")

        elapsed = time.perf_counter() - begin

16:79182c2a8c80

                format_name = f.readline()
                format_name = format_name.rstrip("\n")
        except FileNotFoundError:
            sys.exit(f"ERROR: input tarball missing galaxy/format.txt: {self.pathname}")

        format_map = {
            "axt": "axt",
            "axt+": "axt",
            "cigar": "cigar",
            "differences": "interval",
            "lav": "lav",
            "lav+text": "lav",
            "maf": "maf",
            "maf+": "maf",
            "maf-": "maf",
            "sam": "sam",
            "sam-": "sam",
            "softsam": "sam",
            "softsam-": "sam"
        }

        self.format_name = format_map.get(format_name, "tabular")


class TarRunner:
    def __init__(
        self,

                    found_falures = True

            while not output_queue.empty():
                run_time = output_queue.get()
                run_times.append(run_time)
                if self.debug:
                    print(f"lastz took {run_time}", file=sys.stderr, flush=True)

            if found_falures:
                sys.exit("lastz command failed")

        elapsed = time.perf_counter() - begin