Mercurial > repos > melissacline > xena_import
annotate xena_import.py @ 16:7f03b062f330 default tip
Cleaned up the user interface a bit
| author | melissacline |
|---|---|
| date | Tue, 23 Sep 2014 21:18:54 -0700 |
| parents | a2a7096897a8 |
| children |
| rev | line source |
|---|---|
| 2 | 1 #!/usr/bin/env python |
| 2 | |
| 3 """ | |
| 4 xena_import.py: import a dataset into Xena | |
| 5 | |
| 6 Given a cmdline-specified genomic data file and a cmdline-specified Xena | |
| 7 directory, import the genomic data fle into Xena. This requires assembling | |
| 8 the necessary json file, based on cmdline input. | |
| 9 """ | |
| 10 | |
| 11 import argparse | |
| 12 import json | |
| 9 | 13 import os |
| 2 | 14 import shutil |
| 15 | |
| 16 def main(): | |
| 17 parser = argparse.ArgumentParser() | |
| 18 parser.add_argument("genomicDataPathname", type=str) | |
| 19 parser.add_argument("cohort", type=str) | |
| 20 parser.add_argument("type", type=str) | |
| 21 args = parser.parse_args() | |
| 22 | |
| 3 | 23 xenaBaseDir = os.getenv("XENA_BASE_DIR", "~") |
| 9 | 24 xenaFileDir = xenaBaseDir + "/files" |
| 3 | 25 |
| 2 | 26 # Assemble the metadata in JSON format |
| 27 metadata = { 'cohort': args.cohort, 'type': args.type } | |
| 28 jsonMetadata = json.dumps(metadata, indent=2) | |
| 29 | |
| 30 # Write the metadata to a file in the Xena directory. Use the filename | |
| 31 # of the genomic data file, with an added .json extension. | |
| 32 genomicDataFilename = args.genomicDataPathname.split("/")[-1] | |
| 9 | 33 jsonMetadataPathname = "%s/%s.json" % (xenaFileDir, |
| 2 | 34 genomicDataFilename) |
| 9 | 35 #fp = open("/inside/home/cline/tmp/xena_import.out", "w") |
| 36 #fp.write("xena file dir %s\n" % (xenaFileDir)) | |
| 37 #fp.write("copying metadata to %s and data to %s" % (jsonMetadataPathname, | |
| 38 # xenaFileDir)) | |
| 39 #fp.close() | |
|
6
8d87f0ecc08d
Removed some debugging messages, which I hope we are now done with
melissacline
parents:
3
diff
changeset
|
40 |
| 2 | 41 fp = open(jsonMetadataPathname, "w") |
| 42 fp.write("%s\n" % (jsonMetadata)) | |
| 43 fp.close() | |
| 44 | |
| 45 # Finally, copy the genomic data into the Xena directory | |
| 16 | 46 try: |
| 47 shutil.copy(args.genomicDataPathname, xenaFileDir) | |
| 48 except: | |
| 49 print "Unexpected error", sys.exc_info()[0] | |
| 50 else: | |
| 51 print "Data copied successfully to Xena" | |
| 2 | 52 |
| 53 if __name__ == "__main__": | |
| 54 main() |