Mercurial > repos > melissacline > xena_import
annotate xena_import.py @ 6:8d87f0ecc08d
Removed some debugging messages, which I hope we are now done with
| author | melissacline |
|---|---|
| date | Thu, 04 Sep 2014 15:41:37 -0700 |
| parents | cae2b765ca5d |
| children | a2a7096897a8 |
| 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 | |
| 13 import shutil | |
| 14 | |
| 15 def main(): | |
| 16 parser = argparse.ArgumentParser() | |
| 17 parser.add_argument("genomicDataPathname", type=str) | |
| 18 parser.add_argument("cohort", type=str) | |
| 19 parser.add_argument("type", type=str) | |
| 20 args = parser.parse_args() | |
| 21 | |
| 3 | 22 xenaBaseDir = os.getenv("XENA_BASE_DIR", "~") |
| 23 | |
| 2 | 24 # Assemble the metadata in JSON format |
| 25 metadata = { 'cohort': args.cohort, 'type': args.type } | |
| 26 jsonMetadata = json.dumps(metadata, indent=2) | |
| 27 | |
| 28 # Write the metadata to a file in the Xena directory. Use the filename | |
| 29 # of the genomic data file, with an added .json extension. | |
| 30 genomicDataFilename = args.genomicDataPathname.split("/")[-1] | |
| 31 jsonMetadataPathname = "%s/%s.json" % (args.xenaInputDir, | |
| 32 genomicDataFilename) | |
|
6
8d87f0ecc08d
Removed some debugging messages, which I hope we are now done with
melissacline
parents:
3
diff
changeset
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33 fp = open("/Users/melissacline/tmp/xena.out", "w") |
|
8d87f0ecc08d
Removed some debugging messages, which I hope we are now done with
melissacline
parents:
3
diff
changeset
|
34 fp.write("xena base dir %s\n" % (xenaBaseDir)) |
|
8d87f0ecc08d
Removed some debugging messages, which I hope we are now done with
melissacline
parents:
3
diff
changeset
|
35 fp.write(cmdline) |
|
8d87f0ecc08d
Removed some debugging messages, which I hope we are now done with
melissacline
parents:
3
diff
changeset
|
36 fp.close() |
|
8d87f0ecc08d
Removed some debugging messages, which I hope we are now done with
melissacline
parents:
3
diff
changeset
|
37 |
| 2 | 38 fp = open(jsonMetadataPathname, "w") |
| 39 fp.write("%s\n" % (jsonMetadata)) | |
| 40 fp.close() | |
| 41 | |
| 42 # Finally, copy the genomic data into the Xena directory | |
| 43 shutil.copy(args.genomicDataPathname, args.xenaInputDir) | |
| 44 | |
| 45 if __name__ == "__main__": | |
| 46 main() |