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annotate snippy_core_wrapper.py @ 20:3bbfe41787af draft

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author dfornika
date Fri, 08 Mar 2019 20:46:56 -0500
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1 #!/usr/bin/env python
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2
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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:
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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
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11 # - Builds the snippy-core command
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12 # - Runs the snippy-core command
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13 #
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14 # --------------------------------------
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16 import argparse
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17 import os
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18 import subprocess
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19 from shutil import copyfile
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22 def main():
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24 parser = argparse.ArgumentParser()
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25 parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
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26 parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
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27 args = parser.parse_args()
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29 snippy_core_command_line = ['snippy-core', '--ref', args.ref]
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31 for input_dataset in args.indirs.split(','):
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32 base_name = os.path.basename(input_dataset)
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33 copyfile(input_dataset, base_name)
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34 subprocess.Popen(['tar', '-xf', base_name]).wait()
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36 extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
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37 for extracted_dir in extracted_dirs:
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38 snippy_core_command_line.append(extracted_dir)
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40 subprocess.Popen(snippy_core_command_line).wait()
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43 if __name__ == '__main__':
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44 main()