diff data_manager/FROGS_data_manager.py @ 7:99b2dfb1fa1c draft

planemo upload commit c3ff1475af0e964a0c61458b66e2744c903d8d3d-dirty

--- a/data_manager/FROGS_data_manager.py	Thu Oct 03 10:29:39 2019 -0400
+++ b/data_manager/FROGS_data_manager.py	Fri Oct 04 08:57:45 2019 -0400
@@ -25,13 +25,14 @@
         decoded_content = download.content.decode('utf-8')
         db_index = download.content.splitlines()    
         db_index = [line.split("\t") for line in db_index[1:]]
-        db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[1]]+[line[4]] for line in db_index]  #add column name
+        db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[3]]+[line[4]] for line in db_index]  #add column name
 
     #get frogs dbs
+    os.chdir(target_directory)
     dir_name="frogs_db_"+time.strftime("%Y%m%d")
     os.mkdir(dir_name)
     dbs=set([])
-    for line in db_index[:2]:
+    for line in db_index:
         value=line[4]
         name=value.replace("_"," ")
         link=line[5]
@@ -84,7 +85,6 @@
         phiX_sources(args.resource)
 
     #save info to json file
-    filename = args.output
     open(filename, 'wb').write(to_json_string(data_manager_dict))
 
 if __name__ == "__main__":