From 96a06351052d91ab3b7cf92ec1a539d1ee35af0e Mon Sep 17 00:00:00 2001 From: Bryce Lorenz Kille Date: Fri, 5 Jan 2024 11:29:03 -0600 Subject: [PATCH] Enable MUMi only mode again --- parsnp | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/parsnp b/parsnp index fc76380..fd40ab7 100755 --- a/parsnp +++ b/parsnp @@ -1319,7 +1319,7 @@ SETTINGS: ref = auto_ref lowest_mumi = mumi_dict[idx] mumi_f = "" - if mumi_only and not curated: + if mumi_only: mumi_f = open(os.path.join(outputDir, "config", "recruited_genomes.lst"),'w') @@ -1349,6 +1349,9 @@ SETTINGS: mumi_f.write(os.path.abspath(fnafiles[idx])+",%f"%(mumi_dict[idx])+"\n") finalfiles.append(fnafiles[idx]) allfiles.append(fnafiles[idx]) + if mumi_only: + mumi_f.close() + exit(0) else: try: @@ -1413,10 +1416,6 @@ SETTINGS: if f not in allfiles: allfiles.append(f) - if mumi_only: - mumi_f.close() - sys.exit(1) - # More stuff to autopick the reference if needed: orig_auto_ref = auto_ref if os.path.exists(auto_ref) and autopick_ref: