Mercurial > repos > estrain > data_manager_amrfinderplus

changeset 23:d2931a1c1752 draft

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Uploaded
author estrain
date Mon, 23 May 2022 01:20:20 +0000
parents c3798b25e9d0
children 2cab00532d10
files data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py
diffstat 1 files changed, 4 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py	Sun May 22 23:50:42 2022 +0000
+++ b/data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.py	Mon May 23 01:20:20 2022 +0000
@@ -60,8 +60,6 @@
 
 def print_json (version,argspath,argsname,argsout):
 
-    valueentry="AMRFinderPlus_"+version
-
     data_table_entry = {
       'data_tables' : {
         'amrfinderplus': [
@@ -75,7 +73,6 @@
     }
 
     with open(argsout, 'w') as fh:
-      ##json.dump(data_table_entry,fh, sort_keys=True)
       json.dump(data_table_entry, fh, indent=2, sort_keys=True)
         
 def main():
@@ -86,13 +83,13 @@
 
     args = parser.parse_args()
   
-    os.mkdir("output")
-    os.chdir("output") 
+    os.mkdir("amrdb")
+    os.chdir("amrdb") 
     #Fetch the files and build blast databases
     version=download_from_ncbi()    
     os.chdir("..")
 
-    #shutil.copytree("output",args.path[0])
-    print_json(version,os.path.abspath("output"),args.name[0],args.out[0])
+    #shutil.copytree("amrdb",args.path[0])
+    print_json(version,os.path.abspath("amrdb"),args.name[0],args.out[0])
 
 if __name__ == "__main__": main()