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annotate snippy_core_wrapper.py @ 8:c441153cb4c2 draft

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planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
author dfornika
date Mon, 21 Jan 2019 18:26:12 -0500
parents ab3026667cdc
children caed59c13f82
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3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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1 #!/usr/bin/env python
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3 #--------------------------------------
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4 #
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5 # snippy_core_wrapper.py
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6 #
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7 # This is an intermediary script between snippy-core.xml and snippy-core
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8 # It:
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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9 # - Copys the supplied zipped snippy output files to the working dir
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10 # - Untars them to their datafile name
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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11 # - Builds the snippy-core command
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12 # - Runs the snippy-core command
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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13 #
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14 #--------------------------------------
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16 import os
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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17 import sys
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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18 import argparse
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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19 import subprocess
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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20 from shutil import copyfile
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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22 def main():
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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23 parser = argparse.ArgumentParser()
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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24 parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
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25 parser.add_argument('-i', '--indirs')
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26 args = parser.parse_args()
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28 snippy_core_command_line = ['snippy-core', '--ref', args.ref]
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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30 for indir in args.indirs.split():
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31 base_name = os.path.basename(indir)
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32 sys.stderr.write(indir + '\n')
b9eacd069df6 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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33 copyfile(indir, base_name)
b9eacd069df6 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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34 sys.stderr.write('\n'.join([indir, base_name]) + '\n')
b9eacd069df6 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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35 subprocess.run(['tar', '-xf', base_name])
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37 extracted_dirs = [f.path for f in os.scandir() if f.is_dir() ]
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39 for extracted_dir in extracted_dirs:
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40 snippy_core_command_line.append(extracted_dir)
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42 print(snippy_core_command_line)
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
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43 subprocess.run(snippy_core_command_line)
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45 if __name__ == '__main__':
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46 main()