From 15ad241303d09263d71af29d58081498a76ee355 Mon Sep 17 00:00:00 2001 From: Harrison Deng Date: Fri, 14 Mar 2025 15:24:43 +0000 Subject: [PATCH] Makes use of autoBIGS 0.14.* and fixes CSV export issue caused by missing target. --- pyproject.toml | 2 +- src/autobigs/cli/st.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e3edbd4..fc1810e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ dynamic = ["version"] readme = "README.md" license = {text = "GPL-3.0-or-later"} dependencies = [ - "autoBIGS-engine==0.13.*" + "autoBIGS-engine==0.14.*" ] requires-python = ">=3.12" description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases." diff --git a/src/autobigs/cli/st.py b/src/autobigs/cli/st.py index 20b7457..6ee0590 100644 --- a/src/autobigs/cli/st.py +++ b/src/autobigs/cli/st.py @@ -79,7 +79,7 @@ async def run(args: Namespace): if not isinstance(mlst_profiler, BIGSdbMLSTProfiler): raise TypeError("MLST profiler type invalid") 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, await bigsdb_index.get_scheme_loci(args.seqdefdb, selected_scheme_id)) if len(failed) > 0: print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}") print(f"Completed fetching from {args.seqdefdb} for {scheme_name_lookup[selected_scheme_id]}s for {len(fastas)} sequences.")