ydeng/autoBIGS.cli
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Stop on fail argument now works
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Harrison Deng 2025-02-19 15:50:18 +00:00
parent 319edf36af
commit af9c8c70b8
1 changed files with 1 additions and 1 deletions
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src/autobigs/cli/st.py
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@ -50,7 +50,7 @@ async def run(args: Namespace):
async with BIGSdbIndex() as bigsdb_index: async with BIGSdbIndex() as bigsdb_index:
gen_strings = read_multiple_fastas(args.fastas) gen_strings = read_multiple_fastas(args.fastas)
async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, args.schema) as mlst_profiler: async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, args.schema) as mlst_profiler:
mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings) mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, args.stop_on_fail)
failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out) failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
if len(failed) > 0: if len(failed) > 0:
print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}") print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")