# HG changeset patch
# User estrain
# Date 1646762874 0
# Node ID cac0aa78dad9f7f4fe50448182308d34351e26d8
# Parent  c74ed5f206bd18cc8fa39a1897a0170c670eb1ab
Uploaded

diff -r c74ed5f206bd -r cac0aa78dad9 data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py
--- a/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py	Tue Mar 08 18:07:30 2022 +0000
+++ b/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py	Tue Mar 08 18:07:54 2022 +0000
@@ -43,7 +43,6 @@
     os.system(blastcmd)
 
     for f in pointmuts:
-      print(f)
       blastcmd = "makeblastdb -in " + f +" -dbtype nucl -logfile /dev/null"
       os.system(blastcmd)
 
@@ -59,7 +58,7 @@
     
     return version 
 
-def print_json (version,argspath):
+def print_json (version,argspath,argsname,argsvalue):
 
     valueentry="AMRFinderPlus_"+version
 
@@ -67,8 +66,8 @@
       'data_tables' : {
         'amrfinder_databases': [
           {
-            "value":valueentry,
-            "name":version,
+            "value":argsvalue,
+            "name":argsname,
             "path":argspath,
           }
         ]
@@ -76,12 +75,14 @@
     }
 
     with open("out_file", 'w') as fh:
-      json.dump(data_table_entry,fh, sort_keys=True, indent=2)
+      json.dump(data_table_entry,fh, sort_keys=True)
         
 def main():
    
     parser = argparse.ArgumentParser(description='Download NCBI amrFinderPlus Databases')
-    parser.add_argument('--path', type=str, required=True, nargs=1, help='Absolute Path and database name')
+    parser.add_argument('--name', type=str, required=True, nargs=1, help='Database name')
+    parser.add_argument('--path', type=str, required=True, nargs=1, help='Absolute path to new database folder')
+    parser.add_argument('--value', type=str, required=True, nargs=1, help='Database value')
 
     args = parser.parse_args()
   
@@ -92,6 +93,6 @@
     os.chdir("..")
 
     shutil.copytree("output",args.path[0])
-    print_json(version,args.path[0])
+    print_json(version,args.path[0],args.name[0],args.value[0])
 
 if __name__ == "__main__": main()