Merge branch 'absolute_paths' into 'main'

Absolute paths

See merge request !10

__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)

data/resistance/update_database_resistance.sh

@@ -3,8 +3,8 @@
 PATH_DB=$(dirname "$0")
 DATE=$(date "+%Y-%m-%d")
 ## Update Antimicrobial_resistance/AMRFinderPlus
-wget --quiet --recursive --no-host-directories --cut-dirs=6 ftp://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ -P $PATH_DB/$DATE 
 
+wget --quiet --recursive --no-parent --no-host-directories --cut-dirs=6 -e robots=off https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ -P $PATH_DB/$DATE 
 version_DB=$(cat $PATH_DB/$DATE/version.txt)
 echo "Looking up databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/"
 echo "Downloading AMRFinder database version $version_DB"
@@ -38,6 +38,4 @@ echo -e "Corynebacterium_diphtheriae\tCorynebacterium_diphtheriae\t0" >> $PATH_D
 PATH_DB="$PATH_DB/$DATE" 
 VERSION="$DATE"
 echo "Database directory: '$PATH_DB'"
-echo "Database version: $DATE.1"
-
+echo "Database version: $DATE.1"
\ No newline at end of file
-

module/updating_database.py

@@ -18,5 +18,4 @@ def update_database(arguments, mlst_database:tuple, tox_database:tuple):
         print("   ... done \n")
         
         os.system('bash ' + arguments.path + '/data/resistance/update_database_resistance.sh')
-        print("   ... done \n\n\n")
-        
+        print("   ... done \n\n\n")
\ No newline at end of file
\ No newline at end of file