# HG changeset patch
# User melissacline
# Date 1410822792 14400
# Node ID aa2ed7c6c09b50c071bc3be867b8402867f2034f
Uploaded
diff -r 000000000000 -r aa2ed7c6c09b xenaGetDataset/._xenaGetDataset.py
Binary file xenaGetDataset/._xenaGetDataset.py has changed
diff -r 000000000000 -r aa2ed7c6c09b xenaGetDataset/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xenaGetDataset/tool_dependencies.xml Mon Sep 15 19:13:12 2014 -0400
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diff -r 000000000000 -r aa2ed7c6c09b xenaGetDataset/xenaGetDataset.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xenaGetDataset/xenaGetDataset.py Mon Sep 15 19:13:12 2014 -0400
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+#!/usr/bin/env python
+
+import argparse
+import json
+import urllib2
+import re
+from functools import partial
+
+# import xena query utilities
+import xena_query as xena
+
+# xena url for public datasets, at ucsc
+xena_url = "https://genome-cancer.ucsc.edu/proj/public/xena"
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("datasetType", type=str)
+ parser.add_argument("cohortName", type=str)
+ parser.add_argument("datasetName", type=str)
+ parser.add_argument("outfile", type=str)
+ args = parser.parse_args()
+
+ # short-hand wrappers for xena methods
+ post = xena.compose(json.loads, partial(xena.post, xena_url))
+ find_datasets_type_pattern = xena.compose(post,
+ xena.find_datasets_type_pattern)
+ name_to_url = partial(xena.name_to_url, xena_url)
+
+# Find all TCGA mutation calls by matching on the type and dataset name.
+ fullDatasetName = "%s/%s" % (args.cohortName, args.datasetName)
+ fullDatasetName = "%" + fullDatasetName
+ matchingDatasets = find_datasets_type_pattern(args.datasetType,
+ fullDatasetName)
+ if len(matchingDatasets) > 1:
+ errorMsg = "Error: matches to multiple datasets:"
+ for dataset in matchingDatasets:
+ errorMsg = "%s %s" % (errorMsg, dataset)
+ exit(errorMsg)
+ else:
+ ff = urllib2.urlopen(name_to_url(matchingDatasets[0]))
+ with open(args.outfile, "w") as out:
+ out.write(ff.read())
+
+
+if __name__ == "__main__":
+ main()
+
diff -r 000000000000 -r aa2ed7c6c09b xenaGetDataset/xenaGetDataset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xenaGetDataset/xenaGetDataset.xml Mon Sep 15 19:13:12 2014 -0400
@@ -0,0 +1,35 @@
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+ Retrieve the indicated dataset
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+ xenaGetDataset.py ${datasetType} ${cohortName} ${datasetName} $outFile
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+ Later...
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