comparison run_lastz_tarball.py @ 10:d10e7502aba8 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit effd27b9070dc4564d3cea38869d3bf043201683

9:1ac663f6a344

    output_queue: "queue.Queue[float]",
    debug: bool = False,
) -> None:
    os.chdir("galaxy/files")

    while True:
        command_dict = input_queue.get()

        if not command_dict:
            return

            elapsed = time.perf_counter() - begin
            output_queue.put(elapsed)

        elif p.returncode == 1:
            # should be more robust
            traceback_warning = True

            stderr_file = command_dict["stderr"]
            if stderr_file is None:
                traceback_warning = False
            else:
                with open(stderr_file) as f:
                    for stderr_line in f:
                        for prefix in ["truncating alignment", "truncation can be reduced"]:
                            if stderr_line.startswith(prefix):
                                continue

                        stderr_line = stderr_line.strip()
                        if stderr_line:
                            traceback_warning = False

            if traceback_warning:
                elapsed = time.perf_counter() - begin
                output_queue.put(elapsed)

        try:
            with open("galaxy/format.txt") as f:
                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 ["bam", "maf"]:
            self.format_name = format_name
        elif format_name == "differences":
            self.format_name = "interval"

10:d10e7502aba8

    output_queue: "queue.Queue[float]",
    debug: bool = False,
) -> None:
    os.chdir("galaxy/files")

    # These are not considered errors even though
    # we will end up with a segmented alignment
    truncation_regex = re.compile(
        r"truncating alignment (ending|starting) at \(\d+,\d+\);  anchor at \(\d+,\d+\)$"
    )
    truncation_msg = "truncation can be reduced by using --allocate:traceback to increase traceback memory"

    while True:
        command_dict = input_queue.get()

        if not command_dict:
            return

            elapsed = time.perf_counter() - begin
            output_queue.put(elapsed)

        elif p.returncode == 1:
            traceback_warning = True

            stderr_file = command_dict["stderr"]
            if stderr_file is None:
                traceback_warning = False
            else:
                with open(stderr_file) as f:
                    for stderr_line in f:
                        stderr_line = stderr_line.strip()
                        if (
                            not truncation_regex.match(stderr_line)
                            and stderr_line != truncation_msg
                        ):
                            traceback_warning = False

            if traceback_warning:
                elapsed = time.perf_counter() - begin
                output_queue.put(elapsed)

        try:
            with open("galaxy/format.txt") as f:
                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 ["bam", "maf"]:
            self.format_name = format_name
        elif format_name == "differences":
            self.format_name = "interval"