diff data_manager/data_manager_eggnog.py @ 3:9d94fe7ce8b9 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit e711920c41c8862d7d8133f7b455cf475924e103

--- a/data_manager/data_manager_eggnog.py	Mon Nov 04 16:38:44 2019 -0500
+++ b/data_manager/data_manager_eggnog.py	Tue Nov 05 15:53:42 2019 -0500
@@ -6,8 +6,9 @@
 import json
 import os.path
 import sqlite3
+import sys
 from sqlite3 import OperationalError
-import sys
+
 
 def _get_db_version(sqlitedb_path):
     version = '4.5'
@@ -18,40 +19,47 @@
         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)
+        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='')
+    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') 
+    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', {} )
+    # params = json.loads(open(args.config_file).read())
+    dm_dict = {}
+    dm_dict['data_tables'] = dm_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 )
+    dm_dict['data_tables'][data_table]\
+        = dm_dict['data_tables'].get(data_table, [])
+    data_table_entry = dict(value=db_version, name=db_version,
+                            path=eggnog_db_path)
+    dm_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, [] )
+    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)
-            data_manager_dict['data_tables'][data_table].append( data_table_entry )
+            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( data_manager_dict ) )
+    open(args.config_file, 'wb').write(json.dumps(dm_dict))
+
 
 if __name__ == "__main__":
     main()