.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",

Jenkinsfile

@@ -37,7 +37,7 @@ pipeline {
         }
         stage("publish") {
             environment {
-                CREDS = credentials('4d6f64be-d26d-4f95-8de3-b6a9b0beb311')
+                CREDS = credentials('git.reslate.systems/ydeng')
             }
             when {
                 branch '**/main'

README.md

@@ -1,13 +0,0 @@
-# NSBDiagnosis Toolkit
-
-A software suite automating the diagnostic steps from Sanger Trace Files (ABIFs) and FASTAs. Namely, this tool is (or will be) capable of:
-
-- [ ] Improved consensus conflict resolution via a peak strength metric
-- [ ] Automatic reporting on variations from a reference file
-- [x] Automatic annotating based off pre-existing GenBank data from NCBI
-- [x] Automatic pulling GenBank Data
-- [x] Automatic querying of Institut Pasteur's MLST databases
-- [x] Automatic export of spreadsheet file in the form of a CSV
-- [x] User friendly, and automatable (Galaxy compatible) command-line interface
-- [ ] Interactive Web UI
-

requirements.txt

@@ -2,5 +2,4 @@ aiohttp[speedups]
 biopython
 pytest
 pytest-asyncio
-build
+build
-twine

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)