diff data_manager/fetch_artic_primers.py @ 19:d118e256faca draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/fetch_artic_primers.py	Thu Apr 16 10:19:57 2020 +0000
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+from __future__ import print_function, division
+
+import argparse
+import json
+import os
+import os.path
+import sys
+
+import requests
+
+DATA_TABLE_NAME = 'artic_primers'
+def fetch_artic_primers(output_filename, output_directory, primers):
+    primer_sets = {
+        'ARTICv1': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed',
+        'ARTICv2': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed',
+        'ARTICv3': 'https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed'
+        }
+
+    if not os.path.isdir(output_directory):
+        os.makedirs(output_directory)    
+    data_manager_dict = json.load(open(output_filename))
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables'][DATA_TABLE_NAME] = data_manager_dict['data_tables'].get(DATA_TABLE_NAME, [])
+    
+    data = []
+    for name, url in primer_sets.items():
+        response = requests.get(url)
+        if response.status_code != 200:
+            print('Error: download of', url, 'failed with code', response.status_code, file=sys.stderr)
+            exit(response.status_code)
+        bed_output_filename = os.path.join(output_directory, name + '.bed')
+        open(bed_output_filename, 'w').write(response.text)
+        description = name[:-2] + ' ' + name[-2:] + ' primer set'
+        data.append(dict(value=name, path=bed_output_filename, description=description))
+    data_manager_dict['data_tables'][DATA_TABLE_NAME].extend(data)
+    print(data_manager_dict)
+    json.dump(data_manager_dict, open(output_filename, 'w'))
+
+class SplitArgs(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, values.split(','))
+
+                
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Fetch ARTIC primer files for Galaxy use')
+    parser.add_argument('--output_directory', default='tmp', help='Directory to write output to')
+    parser.add_argument('--galaxy_datamanager_filename', help='Galaxy JSON format file describing data manager inputs')
+    parser.add_argument('--primers', default='ARTCIv1,ARTICv2,ARTICv3', action=SplitArgs, help='Comma separated list of primers to fetch')
+    args = parser.parse_args()
+    fetch_artic_primers(args.galaxy_datamanager_filename, args.output_directory, args.primers)
\ No newline at end of file