From 9ffa3daf3aa501fcce8d9d292d69ed91244ed8a7 Mon Sep 17 00:00:00 2001
From: Martin RETHORET-PASTY <martin.rethoret-pasty@pasteur.fr>
Date: Wed, 7 Feb 2024 15:57:32 +0100
Subject: [PATCH] Replace fasta variable by genome
---
__main__.py | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/__main__.py b/__main__.py
index eece02f..8eebbd9 100644
--- a/__main__.py
+++ b/__main__.py
@@ -342,19 +342,17 @@ if __name__ == "__main__":
basename = os.path.basename(genome)
strain = os.path.splitext(basename)[0]
- fasta = f"{get_path}/{genome}"
- dict_genome = get_species_results(fasta, args.path + '/data/species', str(args.threads))
-
+ dict_genome = get_species_results(genome, args.path + '/data/species', str(args.threads))
if args.mlst :
cd_complex = is_cd_complex(dict_genome)
- dict_genome.update(get_chromosome_mlst_results(MLST_db, fasta, cd_complex, args))
+ dict_genome.update(get_chromosome_mlst_results(MLST_db, genome, cd_complex, args))
if args.tox :
- dict_genome.update(get_tox_results(TOX_db, fasta, args))
+ dict_genome.update(get_tox_results(TOX_db, genome, args))
if args.resistance_virulence :
min_identity = "-1" # Defaut amrfinder
- os.system('amrfinder --nucleotide ' + fasta +
+ os.system('amrfinder --nucleotide ' + genome +
' --name '+strain+
' --nucleotide_output ' + args.outdir + "/" + strain + ".prot.fa" +
' --output '+ args.outdir + "/" + strain + ".blast.out" +
@@ -377,7 +375,7 @@ if __name__ == "__main__":
if args.integron :
os.system('integron_finder --cpu ' + str(args.threads)+
' --outdir '+ args.outdir + "/" +
- ' --gbk --func-annot --mute '+ fasta)
+ ' --gbk --func-annot --mute '+ genome)
os.system('find '+ args.outdir + "/Results_Integron_Finder_*/ " + '-empty -type d -delete')
files = pd.read_csv(args.outdir + "/Results_Integron_Finder_"+strain + "/" + strain+".summary",sep="\t", index_col=0, skiprows = 1)
--
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