comparison scrappie_raw.py @ 3:632c50fe83ba draft default tip

planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a

2:b4721d6ecae2

#!/usr/bin/env python3

import sys, os
import glob
import tarfile
import subprocess
import shutil
import h5py
import numpy as np

    try:
        in_dir = "in_dir"
        if not os.path.exists(in_dir):
            os.makedirs(in_dir)

        tar = tarfile.open(fn, mode='r')
        tar.extractall(path=in_dir)

        files = glob.glob(
            os.path.join(in_dir, "**", "*.fast5"),
            recursive=True
        )

3:632c50fe83ba

#!/usr/bin/env python3

import sys, os
import glob
import subprocess
import shutil
import h5py
import numpy as np

    try:
        in_dir = "in_dir"
        if not os.path.exists(in_dir):
            os.makedirs(in_dir)

        # python's tarfile interface does not sanitize file paths within
        # tarballs, which can be a big security risk. GNU tar does sanitize by
        # default, so it's easier/safer here just to call the system tar
        subprocess.call([
            "tar",
            "-xf",
            fn,
            "-C",
            in_dir])

        files = glob.glob(
            os.path.join(in_dir, "**", "*.fast5"),
            recursive=True
        )