diff efetch.py @ 0:68cd8d564e0a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/efetch.py	Thu Jul 07 02:39:21 2016 -0400
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+import argparse
+import eutils
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='EFetch', epilog='')
+    parser.add_argument('db', help='Database to use')
+    parser.add_argument('--user_email', help="User email")
+    parser.add_argument('--admin_email', help="Admin email")
+
+    # ID source
+    parser.add_argument('--id_list', help='list of ids')
+    parser.add_argument('--id', help='Comma separated individual IDs')
+    parser.add_argument('--history_file', help='Fetch results from previous query')
+
+    # Output
+    parser.add_argument('--retmode', help='Retmode')
+    parser.add_argument('--rettype', help='Rettype')
+    args = parser.parse_args()
+
+    c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
+    merged_ids = c.parse_ids(args.id_list, args.id, args.history_file)
+
+    payload = {}
+    if args.history_file is not None:
+        payload.update(c.get_history())
+    else:
+        payload['id'] = ','.join(merged_ids)
+
+    for attr in ('retmode', 'rettype'):
+        if getattr(args, attr, None) is not None:
+            payload[attr] = getattr(args, attr)
+
+    c.fetch(args.db, ftype=args.retmode, **payload)