Mercurial > repos > jdv > nanopolish

comparison nanopolish_extract.py @ 2:e4b6d4a53f2e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author jdv
date Tue, 03 Oct 2017 21:23:56 -0400
parents 2136c2725fc4
children
comparison
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1:a5db82bec597 2:e4b6d4a53f2e
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
13 out_file = sys.argv[2] 12 out_file = sys.argv[2]
14 threads = sys.argv[3] # currently unused 13 threads = sys.argv[3] # currently unused
15 14
16 extract_fast5(tar_file) 15 extract_fast5(tar_file)
17 16
18 subprocess.call(["nanopolish", 17 subprocess.call([
19 "extract", 18 "nanopolish",
20 "--recurse", 19 "extract",
20 "--recurse",
21 "--fastq", 21 "--fastq",
22 "--output", out_file, 22 "--output", out_file,
23 "in_dir" ]) 23 "in_dir" ])
24 24
25 def extract_fast5(fn): 25 def extract_fast5(fn):
27 try: 27 try:
28 in_dir = "in_dir" 28 in_dir = "in_dir"
29 if not os.path.exists(in_dir): 29 if not os.path.exists(in_dir):
30 os.makedirs(in_dir) 30 os.makedirs(in_dir)
31 31
32 tar = tarfile.open(fn, mode='r') 32 # python's tarfile interface does not sanitize file paths within
33 tar.extractall(path=in_dir) 33 # tarballs, which can be a big security risk. GNU tar does sanitize by
34 # default, so it's easier/safer here just to call the system tar
35 subprocess.call([
36 "tar",
37 "-xf",
38 fn,
39 "-C",
40 "in_dir"])
34 41
35 files = glob.glob( 42 files = glob.glob(
36 os.path.join(in_dir, "**", "*.fast5"), 43 os.path.join(in_dir, "**", "*.fast5"),
37 recursive=True 44 recursive=True
38 ) 45 )