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base: ydeng:afbd883e3e6567f80b0f73ee1c49145cd2334376
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compare: ydeng:f5608b33f979a5b74a2fb7b8dd8061e17327fe06
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ydeng:main

2 Commits
afbd883e3e ... f5608b33f9

Author SHA1 Message Date
Harrison Deng
f5608b33f9 Removed generated file
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2025-01-03 22:51:38 +00:00
Harrison Deng
18b003e0e2 No more error when output folder already exists
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2025-01-03 22:49:00 +00:00
4 changed files with 3 additions and 5 deletions
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2
.gitignore vendored
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@ -356,4 +356,4 @@ package
# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option) # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
src/output.csv output

2
.vscode/launch.json vendored
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@ -6,7 +6,7 @@
"configurations": [ "configurations": [
{ {
"name": "Python Debugger: Current File with Arguments", "name": "CLI ipdbmlst",
"type": "debugpy", "type": "debugpy",
"request": "launch", "request": "launch",
"program": "${workspaceFolder}/src/nsbdiagnosistoolkit/cli/root.py", "program": "${workspaceFolder}/src/nsbdiagnosistoolkit/cli/root.py",

2
output/MLST_20250103204147.csv
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@ -1,2 +0,0 @@
st,clonal-complex,fumC,pepA,icd,adk,pgm,tyrB,glyA
1,ST-2 complex,['1'],['1'],['1'],['1'],['1'],['1'],['1']
1 st clonal-complex fumC pepA icd adk pgm tyrB glyA
2 1 ST-2 complex ['1'] ['1'] ['1'] ['1'] ['1'] ['1'] ['1']

2
src/nsbdiagnosistoolkit/cli/root.py
View File

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