Mercurial > repos > jdv > scrappie

annotate scrappie_raw.py @ 3:632c50fe83ba draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
author jdv
date Tue, 03 Oct 2017 21:50:49 -0400
parents 30c2b84b4117
children
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30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
1 #!/usr/bin/env python3
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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2
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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3 import sys, os
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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4 import glob
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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5 import subprocess
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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6 import shutil
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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7 import h5py
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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8 import numpy as np
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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9
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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10 def main():
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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11 tar_file = sys.argv[1]
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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12 out_file = sys.argv[2]
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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13 threads = sys.argv[3]
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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14
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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15 extract_fast5(tar_file)
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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16 with open(out_file, "w") as outfile:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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17 subprocess.call(["scrappie",
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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18 "raw",
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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19 "--threads", threads,
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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20 "--outformat", "fasta",
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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21 "in_dir" ],
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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22 stdout=outfile )
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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23
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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24 def extract_fast5(fn):
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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25
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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26 try:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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27 in_dir = "in_dir"
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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28 if not os.path.exists(in_dir):
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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29 os.makedirs(in_dir)
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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30
3
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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31 # python's tarfile interface does not sanitize file paths within
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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32 # tarballs, which can be a big security risk. GNU tar does sanitize by
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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33 # default, so it's easier/safer here just to call the system tar
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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34 subprocess.call([
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
parents: 0
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35 "tar",
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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36 "-xf",
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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37 fn,
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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38 "-C",
632c50fe83ba planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit d8cc434bd1704b2834f89b7d91370f356e3ac85a
jdv
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39 in_dir])
0
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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40
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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41 files = glob.glob(
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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42 os.path.join(in_dir, "**", "*.fast5"),
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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43 recursive=True
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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44 )
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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45 if len(files) < 1:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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46 raise ValueError('No FAST5 files found')
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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47 for f in files:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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48 shutil.copy(f, in_dir)
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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49
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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50 except OSError as e:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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51 print("Unexpected error:", e.strerror)
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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52 raise
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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53
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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54 except:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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55 print("Unexpected error:", sys.exc_info()[0])
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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56 raise
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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57
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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58 if __name__ == "__main__" :
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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59 main()