diff gffdm/data_manager/make_json.py @ 0:5ef1c072f07c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gffdm/data_manager/make_json.py	Sun Jun 26 16:53:36 2016 -0400
@@ -0,0 +1,33 @@
+import json
+import argparse
+import os
+import shutil
+
+
+
+parser = argparse.ArgumentParser(description='Create data manager json.')
+parser.add_argument('--dbkey', action='store')
+parser.add_argument('--provider', action='store')
+parser.add_argument('--ref', action='store')
+parser.add_argument('--out', action='store')
+
+args = parser.parse_args()
+
+def main(args):
+    data_manager_entry = {}
+    data_manager_entry['value'] = args.dbkey.lower()
+    data_manager_entry['name'] = args.dbkey
+    data_manager_entry['path'] = '.'
+    data_manager_entry['ref'] = args.ref
+    data_manager_entry['provider'] = args.provider
+    data_manager_json = dict(data_tables=dict(gene_sets=data_manager_entry))
+    params = json.loads(open(args.out).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+    output_path = os.path.join(os.getcwd(), 'featurecount_gxf')
+    for filename in os.listdir(output_path):
+        shutil.move(os.path.join(output_path, filename), target_directory)
+    file(args.output, 'w').write(json.dumps(data_manager_json))
+
+if __name__ == '__main__':
+    main(args)