comparison run_lastz_tarball.py @ 7:4cd7884635c2 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit 869a01abe21b6283d3c83da38fc68761c2e94ba1

6:34d51e66256c

    def __init__(self, pathname: str, debug: bool = False) -> None:
        self.pathname = pathname
        self.debug = debug
        self.tarfile = None
        self.commands: typing.List[typing.Dict[str, typing.Any]] = []
        self._extract()
        self._load_commands()

    def batch_commands(self) -> typing.Iterator[typing.Dict[str, typing.Any]]:
        for command in self.commands:
            yield command

    def _load_commands(self) -> None:
        try:
            f = open("galaxy/commands.json")
        except FileNotFoundError:

                f"ERROR: unexpected json format in line in galaxy/commands.json: {self.pathname}"
            )

        self.commands.append(command_dict)

    def _extract(self) -> None:
        try:
            self.tarball = tarfile.open(
                name=self.pathname, mode="r:*", format=tarfile.GNU_FORMAT
            )
        except FileNotFoundError:
            sys.exit(f"ERROR: unable to find input tarball: {self.pathname}")
        except tarfile.ReadError:
            sys.exit(f"ERROR: error reading input tarball: {self.pathname}")

        begin = time.perf_counter()
        self.tarball.extractall(filter="data")
        self.tarball.close()
        elapsed = time.perf_counter() - begin

        if self.debug:
            print(
                f"Extracted tarball in {elapsed} seconds", file=sys.stderr, flush=True
            )


class TarRunner:
    def __init__(
        self,

        self._cleanup()

    def _cleanup(self) -> None:
        num_output_files = len(self.output_files.keys())

        for file_type, file_list in self.output_files.items():
            with open(f"output.{file_type}", "w") as ofh:
                print("##maf version=1", file=ofh)
                for filename in file_list:
                    with open(f"galaxy/files/{filename}") as ifh:
                        for line in ifh:
                            ofh.write(line)

        if num_output_files == 1:
            file_type = list(self.output_files.keys())[0]
            src_filename = f"output.{file_type}"
            shutil.copy2(src_filename, self.output_pathname)


def main() -> None:
    if not hasattr(tarfile, "data_filter"):
        sys.exit("ERROR: extracting may be unsafe; consider updating Python")

7:4cd7884635c2

    def __init__(self, pathname: str, debug: bool = False) -> None:
        self.pathname = pathname
        self.debug = debug
        self.tarfile = None
        self.commands: typing.List[typing.Dict[str, typing.Any]] = []
        self.format_name = "tabular"
        self._extract()
        self._load_commands()
        self._load_format()

    def batch_commands(self) -> typing.Iterator[typing.Dict[str, typing.Any]]:
        for command in self.commands:
            yield command

    def final_output_format(self) -> str:
        return self.format_name

    def _extract(self) -> None:
        try:
            self.tarball = tarfile.open(
                name=self.pathname, mode="r:*", format=tarfile.GNU_FORMAT
            )
        except FileNotFoundError:
            sys.exit(f"ERROR: unable to find input tarball: {self.pathname}")
        except tarfile.ReadError:
            sys.exit(f"ERROR: error reading input tarball: {self.pathname}")

        begin = time.perf_counter()
        self.tarball.extractall(filter="data")
        self.tarball.close()
        elapsed = time.perf_counter() - begin

        if self.debug:
            print(
                f"Extracted tarball in {elapsed} seconds", file=sys.stderr, flush=True
            )

    def _load_commands(self) -> None:
        try:
            f = open("galaxy/commands.json")
        except FileNotFoundError:

                f"ERROR: unexpected json format in line in galaxy/commands.json: {self.pathname}"
            )

        self.commands.append(command_dict)

    def _load_format(self) -> None:
        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"


class TarRunner:
    def __init__(
        self,

        self._cleanup()

    def _cleanup(self) -> None:
        num_output_files = len(self.output_files.keys())
        if num_output_files != 1:
            sys.exit(f"ERROR: expecting a single output file, found {num_output_files}")

        final_output_format = self.batch_tar.final_output_format()

        for file_type, file_list in self.output_files.items():
            with open(f"output.{final_output_format}", "w") as ofh:
                if final_output_format == "maf":
                    print("##maf version=1", file=ofh)
                for filename in file_list:
                    with open(f"galaxy/files/{filename}") as ifh:
                        for line in ifh:
                            ofh.write(line)

        src_filename = f"output.{final_output_format}"
        shutil.copy2(src_filename, self.output_pathname)

        output_metadata = {
            "output": {
                "ext": final_output_format,
            }
        }

        with open("galaxy.json", "w") as ofh:
            json.dump(output_metadata, ofh)


def main() -> None:
    if not hasattr(tarfile, "data_filter"):
        sys.exit("ERROR: extracting may be unsafe; consider updating Python")