diff uniprotkb.py @ 8:3f6354b7eb94 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniprotkb.py	Tue Sep 27 13:21:28 2022 +0000
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+
+import requests
+
+uniprotkb_url = 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta&query='
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='Retrieve Uniprot data using streaming')
+    parser.add_argument('-u', '--url', help="Uniprot rest api URL")
+    parser.add_argument('-q', '--query', help="UniprotKB Query")
+    parser.add_argument('-o', '--output', type=argparse.FileType('wb'), default=sys.stdout, help='data')
+    parser.add_argument('-d', '--debug', action='store_true', help='Debug')
+    args = parser.parse_args()
+    if args.url:
+        url = args.url
+    else:
+        url = uniprotkb_url + args.query
+    with requests.get(url, stream=True) as request:
+        request.raise_for_status()
+        for chunk in request.iter_content(chunk_size=2**20):
+            args.output.write(chunk)
+
+
+if __name__ == "__main__":
+    __main__()