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1 #!/usr/bin/env python
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2
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3 """
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4 xena_import.py: import a dataset into Xena
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5
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6 Given a cmdline-specified genomic data file and a cmdline-specified Xena
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7 directory, import the genomic data fle into Xena. This requires assembling
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8 the necessary json file, based on cmdline input.
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9 """
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10
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11 import argparse
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12 import json
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13 import shutil
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14
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15 def main():
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16 parser = argparse.ArgumentParser()
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17 parser.add_argument("genomicDataPathname", type=str)
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18 parser.add_argument("cohort", type=str)
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19 parser.add_argument("type", type=str)
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20 args = parser.parse_args()
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21
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3
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22 xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
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23
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2
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24 # Assemble the metadata in JSON format
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25 metadata = { 'cohort': args.cohort, 'type': args.type }
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26 jsonMetadata = json.dumps(metadata, indent=2)
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27
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28 # Write the metadata to a file in the Xena directory. Use the filename
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29 # of the genomic data file, with an added .json extension.
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30 genomicDataFilename = args.genomicDataPathname.split("/")[-1]
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31 jsonMetadataPathname = "%s/%s.json" % (args.xenaInputDir,
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32 genomicDataFilename)
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33 fp = open(jsonMetadataPathname, "w")
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34 fp.write("%s\n" % (jsonMetadata))
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35 fp.close()
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36
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37 # Finally, copy the genomic data into the Xena directory
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38 shutil.copy(args.genomicDataPathname, args.xenaInputDir)
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39
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40 if __name__ == "__main__":
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41 main()
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