Mercurial > repos > melissacline > xena_import
view xena_import.py @ 2:b3cd322f7749
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author | melissacline |
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date | Wed, 03 Sep 2014 15:34:45 -0400 |
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children | cae2b765ca5d |
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#!/usr/bin/env python """ xena_import.py: import a dataset into Xena Given a cmdline-specified genomic data file and a cmdline-specified Xena directory, import the genomic data fle into Xena. This requires assembling the necessary json file, based on cmdline input. """ import argparse import json import shutil def main(): parser = argparse.ArgumentParser() parser.add_argument("genomicDataPathname", type=str) parser.add_argument("cohort", type=str) parser.add_argument("type", type=str) parser.add_argument("xenaInputDir", type=str) args = parser.parse_args() # Assemble the metadata in JSON format metadata = { 'cohort': args.cohort, 'type': args.type } jsonMetadata = json.dumps(metadata, indent=2) # Write the metadata to a file in the Xena directory. Use the filename # of the genomic data file, with an added .json extension. genomicDataFilename = args.genomicDataPathname.split("/")[-1] jsonMetadataPathname = "%s/%s.json" % (args.xenaInputDir, genomicDataFilename) fp = open(jsonMetadataPathname, "w") fp.write("%s\n" % (jsonMetadata)) fp.close() # Finally, copy the genomic data into the Xena directory shutil.copy(args.genomicDataPathname, args.xenaInputDir) if __name__ == "__main__": main()