diff data_manager/data_manager_eggnog.py @ 2:a74d61dbd155 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_eggnog.py	Mon Nov 04 16:38:44 2019 -0500
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import json
+import os.path
+import sqlite3
+from sqlite3 import OperationalError
+import sys
+
+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() )
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_table = 'eggnog_mapper_db'
+    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
+    data_table_entry = dict(value=db_version, name=db_version, path=eggnog_db_path)
+    data_manager_dict['data_tables'][data_table].append( data_table_entry )
+    data_table = 'eggnog_mapper_hmm_dbs'
+    data_manager_dict['data_tables'][data_table] = data_manager_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)
+            data_manager_dict['data_tables'][data_table].append( data_table_entry )
+
+    # save info to json file
+    open( args.config_file, 'wb' ).write( json.dumps( data_manager_dict ) )
+
+if __name__ == "__main__":
+    main()