Mercurial > repos > melissacline > xena_import
comparison xena_import.py @ 3:cae2b765ca5d
Changing how the Xena base dir is communicated
| author | melissacline |
|---|---|
| date | Wed, 03 Sep 2014 16:02:24 -0700 |
| parents | b3cd322f7749 |
| children | 8d87f0ecc08d |
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| 2:b3cd322f7749 | 3:cae2b765ca5d |
|---|---|
| 15 def main(): | 15 def main(): |
| 16 parser = argparse.ArgumentParser() | 16 parser = argparse.ArgumentParser() |
| 17 parser.add_argument("genomicDataPathname", type=str) | 17 parser.add_argument("genomicDataPathname", type=str) |
| 18 parser.add_argument("cohort", type=str) | 18 parser.add_argument("cohort", type=str) |
| 19 parser.add_argument("type", type=str) | 19 parser.add_argument("type", type=str) |
| 20 parser.add_argument("xenaInputDir", type=str) | |
| 21 args = parser.parse_args() | 20 args = parser.parse_args() |
| 21 | |
| 22 xenaBaseDir = os.getenv("XENA_BASE_DIR", "~") | |
| 22 | 23 |
| 23 # Assemble the metadata in JSON format | 24 # Assemble the metadata in JSON format |
| 24 metadata = { 'cohort': args.cohort, 'type': args.type } | 25 metadata = { 'cohort': args.cohort, 'type': args.type } |
| 25 jsonMetadata = json.dumps(metadata, indent=2) | 26 jsonMetadata = json.dumps(metadata, indent=2) |
| 26 | 27 |