Mercurial > repos > jdv > scrappie

annotate 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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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 tarfile
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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6 import subprocess
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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7 import shutil
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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8 import h5py
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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9 import numpy as np
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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11 def main():
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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12 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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13 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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14 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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30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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16 extract_fast5(tar_file)
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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17 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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18 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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19 "raw",
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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20 "--threads", threads,
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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21 "--outformat", "fasta",
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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22 "in_dir" ],
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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23 stdout=outfile )
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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24
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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25 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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30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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27 try:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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28 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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29 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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30 os.makedirs(in_dir)
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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31
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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32 tar = tarfile.open(fn, mode='r')
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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33 tar.extractall(path=in_dir)
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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34
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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35 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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36 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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37 recursive=True
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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38 )
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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39 if len(files) < 1:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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40 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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41 for f in files:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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42 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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43
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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44 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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45 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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46 raise
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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47
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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48 except:
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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49 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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50 raise
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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51
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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52 if __name__ == "__main__" :
30c2b84b4117 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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53 main()