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annotate zipcollection.py @ 0:fe887de9b4b5 draft

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planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
author stevecassidy
date Thu, 16 Nov 2017 06:19:53 -0500
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children 278da6e5ab11
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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diff changeset
1 from __future__ import print_function
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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2 import argparse
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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3 from zipfile import ZipFile
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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5 def parser():
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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diff changeset
6 parser = argparse.ArgumentParser(description="Find matching segments in a TextGrid")
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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7 parser.add_argument('--dataset', required=True, action="store", type=str, help="TextGrid files (comma separated)")
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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8 parser.add_argument('--identifier', required=True, action="store", type=str, help="Dataset identifiers (comma separated)")
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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9 parser.add_argument('--output', required=True, action="store", type=str, help="Path to output file")
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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10 return parser.parse_args()
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
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13 def main():
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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14 args = parser()
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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16 datasets = args.dataset.split(',')
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
diff changeset
17 identifiers = args.identifier.split(',')
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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18 assert len(datasets) == len(identifiers), "number of datasets must match number of identifiers"
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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20 pairs = zip(datasets, identifiers)
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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22 with ZipFile(args.output, 'w') as zipfile:
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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23 for dataset, identifier in pairs:
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
diff changeset
24 zipfile.write(dataset, identifier)
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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27 if __name__ == '__main__':
fe887de9b4b5 planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
stevecassidy
parents:
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28 main()