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annotate nanopolish_extract.py @ 6:36cc4ae4160e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d47b131af7d3a9f8446732f91ec08503c99aab58
author jdv
date Mon, 04 Dec 2017 02:03:21 -0500
parents e4b6d4a53f2e
children
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2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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1 #!/usr/bin/env python3
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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2
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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3 import sys, os
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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4 import glob
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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5 import subprocess
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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6 import shutil
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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7 import h5py
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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8 import numpy as np
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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9
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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10 def main():
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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11 tar_file = sys.argv[1]
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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12 out_file = sys.argv[2]
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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13 threads = sys.argv[3] # currently unused
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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14
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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15 extract_fast5(tar_file)
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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16
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e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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17 subprocess.call([
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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18 "nanopolish",
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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19 "extract",
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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20 "--recurse",
0
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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21 "--fastq",
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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22 "--output", out_file,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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23 "in_dir" ])
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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24
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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25 def extract_fast5(fn):
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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26
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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27 try:
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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28 in_dir = "in_dir"
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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29 if not os.path.exists(in_dir):
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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30 os.makedirs(in_dir)
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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31
2
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jdv
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32 # python's tarfile interface does not sanitize file paths within
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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33 # tarballs, which can be a big security risk. GNU tar does sanitize by
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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34 # default, so it's easier/safer here just to call the system tar
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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35 subprocess.call([
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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36 "tar",
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
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37 "-xf",
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
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38 fn,
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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39 "-C",
e4b6d4a53f2e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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40 "in_dir"])
0
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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41
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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42 files = glob.glob(
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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43 os.path.join(in_dir, "**", "*.fast5"),
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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44 recursive=True
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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45 )
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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46 if len(files) < 1:
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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47 raise ValueError('No FAST5 files found')
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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48
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49 except OSError as e:
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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50 print("Unexpected error:", e.strerror)
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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51 raise
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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52
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53 except:
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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54 print("Unexpected error:", sys.exc_info()[0])
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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55 raise
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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56
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57 if __name__ == "__main__" :
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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58 main()