Mercurial > repos > jdv > nanonet

comparison nanonet_1D.py @ 2:3f35881c2e25 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author jdv
date Tue, 03 Oct 2017 20:51:59 -0400
parents decd5688d719
children
comparison
equal deleted inserted replaced
1:57447db0ec78 2:3f35881c2e25
1 #!/usr/bin/env python3 1 #!/usr/bin/env python3
2 2
3 import sys, os 3 import sys, os
4 import glob 4 import glob
5 import tarfile
6 import subprocess 5 import subprocess
7 import shutil 6 import shutil
8 import h5py 7 import h5py
9 import numpy as np 8 import numpy as np
10 9
26 try: 25 try:
27 in_dir = "in_dir" 26 in_dir = "in_dir"
28 if not os.path.exists(in_dir): 27 if not os.path.exists(in_dir):
29 os.makedirs(in_dir) 28 os.makedirs(in_dir)
30 29
31 tar = tarfile.open(fn, mode='r') 30 # python's tarfile interface does not sanitize file paths within
32 tar.extractall(path=in_dir) 31 # tarballs, which can be a big security risk. GNU tar does sanitize by
32 # default, so it's easier/safer here just to call the system tar
33 subprocess.call([
34 "tar",
35 "-xf",
36 fn,
37 "-C",
38 in_dir])
33 39
34 files = glob.glob( 40 files = glob.glob(
35 os.path.join(in_dir, "**", "*.fast5"), 41 os.path.join(in_dir, "**", "*.fast5"),
36 recursive=True 42 recursive=True
37 ) 43 )