diff data_manager/ariba_database_builder.py @ 0:a8bb47cc7625 draft

planemo upload for repository tbd commit 0af229dbbda0496819ca95938c2e0628db689134

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/ariba_database_builder.py	Tue Jan 08 11:04:25 2019 -0500
@@ -0,0 +1,33 @@
+# Thanh Le Viet
+# 7-Jan-2019
+
+import argparse
+import json
+import os
+import shutil
+
+
+def main(args):
+    output_path = os.getcwd()
+    db_folder = [d for d in os.listdir(output_path) if os.path.isdir(d)]
+    params = json.loads(open(args.output).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+    data_manager_entry = []
+    for db in db_folder:
+        # print("Current: ".format(os.path.join(output_path, d)))
+        # print("Target: {}".format(target_directory))
+        shutil.move(os.path.join(output_path, d), os.path.join(target_directory, d))
+        data_manager_entry.append(dict(value=db.lower(),
+                                  name=db,
+                                  path=target_directory)
+                                    )
+    data_manager_json = dict(data_tables=dict(ariba_databases=data_manager_entry))
+    file(args.output, 'w').write(json.dumps(data_manager_json))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Create data manager json.')
+    parser.add_argument('--out', dest='output', action='store', help='JSON filename')
+    args = parser.parse_args()
+    main(args)
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