From eac94f8c279bb9bffe2decbe223549ebcb9e3110 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 10 Dec 2020 10:44:07 +0100
Subject: [PATCH] if info_file given, check that it exists
if info file given, but not 'only_mash', a new infofile will be generated. To avoid overwrite it, we first rename the given info_file with .bak suffix. But before that, check that the given file exists. If not, no need to rename.
---
PanACoTA/subcommands/prepare.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py
index 05e145dd..00b45d6a 100644
--- a/PanACoTA/subcommands/prepare.py
+++ b/PanACoTA/subcommands/prepare.py
@@ -184,7 +184,7 @@ def main(cmd, NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_ref
# Not only mash, so a new info file will be created. If the user still gave an info
# file (he will be warned that it will be ignored), rename it with '.bak'
# to avoid erasing it
- if info_file:
+ if info_file and os.path.isfile(info_file):
os.rename(info_file, info_file + ".back")
# 'no_refseq = True" : Do not download genomes, just do QC and mash filter on given genomes
@@ -492,7 +492,7 @@ def check_args(parser, args):
print(colored(thresholds_message(args.l90, args.nbcont), "yellow"))
# Warn if user gave info file, but does not ask to run only Mash -> info file will be ignored
- if args.info_file and not args.only_mash:
+ if (args.info_file and not args.only_mash) or (args.info_file and not args.no_refseq):
message = (" !! You gave an info file (--info option), but did not ask to run only Mash "
"step (-M option). Your info file will be ignored (and renamed with '.back' "
"at the end), and another one will "
--
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