comparison run_lastz_tarball.py @ 6:34d51e66256c draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit 2ab3532f7a45153eb0f945ac22c37cdcaea8c1e1

5:a68e128cdb1a

import multiprocessing
import os
import queue
import re
import shutil
import sys
import subprocess
import tarfile
import tempfile
import typing
import time


lastz_output_format_regex = re.compile(
    r"^(?:axt\+?|blastn|cigar|differences|general-?.+|lav|lav\+text|maf[-+]?|none|paf(?::wfmash)?|rdotplot|sam-?|softsam-?|text)$",
    re.IGNORECASE,

        else:
            stderr = command_dict["stderr"]
            if stderr is not None:
                try:
                    statinfo = os.stat(stderr, follow_symlinks=False)
                except:
                    statinfo = None

                if statinfo is None:
                    sys.exit(f"unable to stat stderr file: {' '.join(args)}")

    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:
                for filename in file_list:
                    with open(f"galaxy/files/{filename}") as ifh:
                        for line in ifh:
                            ofh.write(line)

6:34d51e66256c

import multiprocessing
import os
import queue
import re
import shutil
import subprocess
import sys
import tarfile
import tempfile
import time
import typing


lastz_output_format_regex = re.compile(
    r"^(?:axt\+?|blastn|cigar|differences|general-?.+|lav|lav\+text|maf[-+]?|none|paf(?::wfmash)?|rdotplot|sam-?|softsam-?|text)$",
    re.IGNORECASE,

        else:
            stderr = command_dict["stderr"]
            if stderr is not None:
                try:
                    statinfo = os.stat(stderr, follow_symlinks=False)
                except Exception:
                    statinfo = None

                if statinfo is None:
                    sys.exit(f"unable to stat stderr file: {' '.join(args)}")

    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)