Mercurial > repos > melissacline > ucsc_xena_platform

diff xena_import.py @ 49:8da6920a39ac

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add hg19 assembly in xena_import
author jingchunzhu
date Sun, 09 Aug 2015 23:23:58 -0700
parents 1ef1886dae04
children
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line diff
--- a/xena_import.py	Sun Aug 09 22:39:09 2015 -0700
+++ b/xena_import.py	Sun Aug 09 23:23:58 2015 -0700
@@ -54,6 +54,7 @@
     parser.add_argument("--label", type=str, default=None)
     parser.add_argument("--colNormalization", type=bool, default=False)
     parser.add_argument("--probeMap", type=str, default=None)
+    parser.add_argument("--assembly", type=str, default=None)
     args = parser.parse_args()
 
     fp2 = open(args.outfile, "w")
@@ -90,7 +91,8 @@
             updateColNormalization(metadata)
         if args.probeMap is not None:
             metadata[':probeMap'] = probeMapDataFile
-            
+        if args.assembly:
+            metadata['assembly'] = args.assembly
         jsonMetadata = json.dumps(metadata, indent=2) 
         fp = open(jsonMetadataTargetPathname, "w")
         fp.write("%s\n" % (jsonMetadata))