Mercurial > repos > jdv > nanonet

annotate 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
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
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1 #!/usr/bin/env python3
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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2
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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3 import sys, os
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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4 import glob
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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5 import subprocess
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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6 import shutil
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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7 import h5py
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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8 import numpy as np
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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9
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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10 def main():
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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11 tar_file = sys.argv[1]
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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12 out_file = sys.argv[2]
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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13 threads = sys.argv[3]
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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14
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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15 extract_fast5(tar_file)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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17 subprocess.call(["nanonetcall",
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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18 "--jobs", threads,
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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19 "--fastq",
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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20 "--output", out_file,
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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21 "in_dir" ])
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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22
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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23 def extract_fast5(fn):
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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24
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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25 try:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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26 in_dir = "in_dir"
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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27 if not os.path.exists(in_dir):
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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28 os.makedirs(in_dir)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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29
2
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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30 # python's tarfile interface does not sanitize file paths within
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 0
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31 # tarballs, which can be a big security risk. GNU tar does sanitize by
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 0
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32 # default, so it's easier/safer here just to call the system tar
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 0
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33 subprocess.call([
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 0
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34 "tar",
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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35 "-xf",
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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36 fn,
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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37 "-C",
3f35881c2e25 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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38 in_dir])
0
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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39
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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40 files = glob.glob(
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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41 os.path.join(in_dir, "**", "*.fast5"),
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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42 recursive=True
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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43 )
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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44 if len(files) < 1:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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45 raise ValueError('No FAST5 files found')
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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46 for f in files:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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47 shutil.copy(f, in_dir)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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48
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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49 except OSError as e:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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50 print("Unexpected error:", e.strerror)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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51 raise
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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52
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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53 except:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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54 print("Unexpected error:", sys.exc_info()[0])
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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55 raise
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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56
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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57 if __name__ == "__main__" :
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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58 main()