.gitignore

@@ -356,4 +356,4 @@ package
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
-output
+src/output.csv

.vscode/launch.json

@@ -6,7 +6,7 @@
     "configurations": [
         
         {
-            "name": "CLI ipdbmlst",
+            "name": "Python Debugger: Current File with Arguments",
             "type": "debugpy",
             "request": "launch",
             "program": "${workspaceFolder}/src/nsbdiagnosistoolkit/cli/root.py",

output/MLST_20250103204147.csv

@@ -0,0 +1,2 @@
+st,clonal-complex,fumC,pepA,icd,adk,pgm,tyrB,glyA
+1,ST-2 complex,['1'],['1'],['1'],['1'],['1'],['1'],['1']

src/nsbdiagnosistoolkit/cli/root.py

@@ -58,7 +58,7 @@ parser.add_argument(
 def cli():
     args = parser.parse_args()
     gen_strings = aggregator.aggregate_sequences(args.fastas, args.abifs)
-    os.makedirs(args.out, exist_ok=True)
+    os.makedirs(args.out)
     if args.institut_pasteur_db is not None:
         mlst_profiles = aggregator.profile_all_genetic_strings(
             gen_strings, args.institut_pasteur_db)