diff data_manager/data_manager_eggnog.py @ 0:6d8144eef202 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_eggnog.py	Mon Nov 11 11:49:16 2019 -0500
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import json
+import os.path
+import sqlite3
+import sys
+from sqlite3 import OperationalError
+
+
+def _get_db_version(sqlitedb_path):
+    version = '4.5'
+    try:
+        query = 'select version from version'
+        conn = sqlite3.connect(sqlitedb_path)
+        cur = conn.cursor()
+        cur.execute(query)
+        version = cur.fetchone()[0]
+    except OperationalError as e:
+        print('Assuming eggnog version %s because %s   %s' %
+              (version, sqlitedb_path, e), file=sys.stderr)
+    return version
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--config_file')
+    parser.add_argument('--install_path')
+    parser.add_argument('--dbs', default='')
+    args = parser.parse_args()
+
+    eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
+    if not os.path.exists(eggnog_db_path):
+        print('Can not open: %s' % eggnog_db_path, file=sys.stderr)
+        exit(1)
+    db_version = _get_db_version(eggnog_db_path)
+
+    # params = json.loads(open(args.config_file).read())
+    dm_dict = {}
+    dm_dict['data_tables'] = dm_dict.get('data_tables', {})
+    data_table = 'eggnog_mapper_db'
+    dm_dict['data_tables'][data_table]\
+        = dm_dict['data_tables'].get(data_table, [])
+    data_table_entry = dict(value=db_version, name=db_version,
+                            path=args.install_path)
+    dm_dict['data_tables'][data_table].append(data_table_entry)
+    data_table = 'eggnog_mapper_hmm_dbs'
+    dm_dict['data_tables'][data_table]\
+        = dm_dict['data_tables'].get(data_table, [])
+    if args.dbs:
+        dbs = [x.strip() for x in args.dbs.split(',')]
+        for db in dbs:
+            key = '%s_%s' % (db_version, db)
+            data_table_entry = dict(key=key, db_version=db_version,
+                                    value=db, name=db, path=db)
+            dm_dict['data_tables'][data_table].append(data_table_entry)
+
+    # save info to json file
+    open(args.config_file, 'wb').write(json.dumps(dm_dict))
+
+
+if __name__ == "__main__":
+    main()