Mercurial > repos > jdv > scrappie

comparison scrappie_raw.py @ 0:30c2b84b4117 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
author jdv
date Wed, 30 Aug 2017 02:55:35 -0400
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children 632c50fe83ba
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-1:000000000000 0:30c2b84b4117
1 #!/usr/bin/env python3
2
3 import sys, os
4 import glob
5 import tarfile
6 import subprocess
7 import shutil
8 import h5py
9 import numpy as np
10
11 def main():
12 tar_file = sys.argv[1]
13 out_file = sys.argv[2]
14 threads = sys.argv[3]
15
16 extract_fast5(tar_file)
17 with open(out_file, "w") as outfile:
18 subprocess.call(["scrappie",
19 "raw",
20 "--threads", threads,
21 "--outformat", "fasta",
22 "in_dir" ],
23 stdout=outfile )
24
25 def extract_fast5(fn):
26
27 try:
28 in_dir = "in_dir"
29 if not os.path.exists(in_dir):
30 os.makedirs(in_dir)
31
32 tar = tarfile.open(fn, mode='r')
33 tar.extractall(path=in_dir)
34
35 files = glob.glob(
36 os.path.join(in_dir, "**", "*.fast5"),
37 recursive=True
38 )
39 if len(files) < 1:
40 raise ValueError('No FAST5 files found')
41 for f in files:
42 shutil.copy(f, in_dir)
43
44 except OSError as e:
45 print("Unexpected error:", e.strerror)
46 raise
47
48 except:
49 print("Unexpected error:", sys.exc_info()[0])
50 raise
51
52 if __name__ == "__main__" :
53 main()