Mercurial > repos > melissacline > ucsc_xena_platform
annotate xenaGetDataset.py @ 41:02b0824c7d60
Download data from any hub in the federated xena platform
| author | jingchunzhu <jingchunzhu@gmail.com> |
|---|---|
| date | Mon, 27 Jul 2015 10:05:22 -0700 |
| parents | 8bb037f88ed2 |
| children | 3167c1a26101 |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 | |
| 3 import argparse | |
| 4 import re | |
| 5 import urllib2 | |
| 6 | |
| 7 | |
| 8 def main(): | |
| 9 parser = argparse.ArgumentParser() | |
| 10 parser.add_argument("dataHub", type=str) | |
| 11 parser.add_argument("datasetId", type=str) | |
|
41
02b0824c7d60
Download data from any hub in the federated xena platform
jingchunzhu <jingchunzhu@gmail.com>
parents:
0
diff
changeset
|
12 #parser.add_argument("metadatafile", type=str) |
| 0 | 13 parser.add_argument("datafile", type=str) |
| 14 args = parser.parse_args() | |
| 15 | |
| 16 datasetUrlHost = re.sub("/proj/", "/download/", args.dataHub) | |
| 17 datasetIdTokens = re.split("/", args.datasetId) | |
| 18 datasetUrl = datasetUrlHost + "/" + "/".join(datasetIdTokens[1:]) | |
| 19 print datasetUrl | |
|
41
02b0824c7d60
Download data from any hub in the federated xena platform
jingchunzhu <jingchunzhu@gmail.com>
parents:
0
diff
changeset
|
20 """ |
| 0 | 21 metadataUrl = datasetUrl + ".json" |
| 22 mm = urllib2.urlopen(metadataUrl) | |
| 23 with open(args.metadatafile, "w") as metadata: | |
| 24 metadata.write(mm.read()) | |
| 25 mm.close() | |
|
41
02b0824c7d60
Download data from any hub in the federated xena platform
jingchunzhu <jingchunzhu@gmail.com>
parents:
0
diff
changeset
|
26 """ |
| 0 | 27 dd = urllib2.urlopen(datasetUrl) |
| 28 with open(args.datafile, "w") as data: | |
| 29 data.write(dd.read()) | |
| 30 dd.close() | |
| 31 | |
| 32 | |
| 33 if __name__ == "__main__": | |
| 34 main() | |
| 35 |