Merge branch 'master' of https://github.com/ntoda03/NLGenomeSweeper

README.md

@@ -3,8 +3,11 @@ Identification of NBS-LRR genes in genomic sequences
 v.1.0
 
 This was created as part of the project HealthyGrape2 at the INRA.
+
 [email protected] (out-of-date)
 
+[email protected] (current)
+
 ## Introduction
 NLGenomeSweeper is a command line bash pipeline that searches a genome for NBS-LRR (NLR) disease resistance 
 genes based on the presence of the NB-ARC domain using the consensus sequence of the Pfam HMM profile (PF00931) 
@@ -18,7 +21,11 @@ genes. Therefore, it is primarily for the identification of NLR genes for a geno
 exists or a large number of genes are expected to be absent due to repeat masking and difficulties in annotation. 
 For many genomes this may be the case. 
 
-If you use NLGenomeSweeper for published research, please cite the paper (coming soon). Thanks!
+If you use NLGenomeSweeper for published research, please cite the paper. 
+
+Toda, N.; Rustenholz, C.; Baud, A.; Paslier, M.-C.L.; Amselem, J.; Merdinoglu, D.; Faivre-Rampant, P. [NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification. Genes 2020, 11, 333.](https://www.mdpi.com/2073-4425/11/3/333)
+
+Thanks!
 
 ## Obtaining NLGenomeSweeper
 NLGenomeSweeper can be obtained from the [GitHub page](https://github.com/ntoda03/NLGenomeSweeper)
@@ -55,6 +62,8 @@ Required arguments:
 Input arguments (optional):
 
   -consensus <fasta file>                     Also search the genome using a custom NB-ARC consensus sequence(s).
+                                  This is a protein fasta file of the domain sequence(s) only.
+                                  Not recommended.
 
 Output arguments (optional):
 

scripts/CustomProfiler.py

@@ -31,7 +31,7 @@
 # Folder created in output dir for results
 profile_folder = '00_profile_creation'
 # Location of the Pfam NB-ARC hmm profile within the program directory
-nbarc_location = "data/pfam_NB-ARC.hmm"
+nbarc_location = "data/Vitis_vinifera_NB-ARC_consensus.fa"
 
 
 ##########################################################################
@@ -80,8 +80,8 @@ def main(argv):
 		os.mkdir(args.outdir + profile_folder)
 
 	# Run program 
-	subprocess.run('{}/createProfile.sh {} {} {} {} {} prot'.format( program_dir, program_dir + '/' + nbarc_location, 
-		args.verified, args.outdir + profile_folder + '/', program_dir, args.prefix), shell=True)
+	subprocess.run('{}/createProfile.sh {} {} {} {} {} prot'.format( program_dir, args.verified,  
+		 args.outdir + profile_folder + '/', program_dir, args.prefix, program_dir + '/' + nbarc_location, "prot"), shell=True)
 
 if __name__ == "__main__":
    main(sys.argv[1:])