comparison xena_import.py @ 9:a2a7096897a8

FIXED the xena import process

8:dc42b6bbc22b

  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)
    args = parser.parse_args()

    xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")

    # 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("/Users/melissacline/tmp/xena.out", "w")
    fp.write("xena base dir %s\n" % (xenaBaseDir))
    fp.write(cmdline)
    fp.close()

    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()

9:a2a7096897a8

  the necessary json file, based on cmdline input.
"""

import argparse
import json
import os
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)
    args = parser.parse_args()

    xenaBaseDir = os.getenv("XENA_BASE_DIR", "~")
    xenaFileDir = xenaBaseDir + "/files"

    # 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" % (xenaFileDir, 
                                           genomicDataFilename)
    #fp = open("/inside/home/cline/tmp/xena_import.out", "w")
    #fp.write("xena file dir %s\n" % (xenaFileDir))
    #fp.write("copying metadata to %s and data to %s" % (jsonMetadataPathname, 
    #                                                    xenaFileDir))
    #fp.close()

    fp = open(jsonMetadataPathname, "w")
    fp.write("%s\n" % (jsonMetadata))
    fp.close()

    # Finally, copy the genomic data into the Xena directory
    shutil.copy(args.genomicDataPathname, xenaFileDir)

if __name__ == "__main__":
    main()