From 70f1a29ce97be92b811256c3b256879f9113ab32 Mon Sep 17 00:00:00 2001
From: ljacquin <jacquin.julien@gmail.com>
Date: Wed, 17 Apr 2024 14:25:55 +0200
Subject: [PATCH] update: format .sh scripts

---
 clean_scans.sh                      |  2 +-
 get_results_scans.sh                | 36 ++++++++++++++---------------
 khamix.sh                           | 34 +++++++++++++--------------
 make_scripts_programs_executable.sh |  2 +-
 programs/scan_chromo_num_k.sh       | 16 ++++++-------
 5 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/clean_scans.sh b/clean_scans.sh
index 57e899e..5fe1899 100755
--- a/clean_scans.sh
+++ b/clean_scans.sh
@@ -6,6 +6,6 @@ rm -r genome_scan_chromo_num*
 rm -r results_genome_scan
 rm data_parameters/kernel_index.txt
 rm data_parameters/nb_snp_hap.txt
-rm data_parameters/nb_chromosomes.txt 
+rm data_parameters/nb_chromosomes.txt
 rm data_parameters/trait_name.txt
 rm data_parameters/signif_level.txt
diff --git a/get_results_scans.sh b/get_results_scans.sh
index 269a753..ef5a9e6 100755
--- a/get_results_scans.sh
+++ b/get_results_scans.sh
@@ -11,8 +11,8 @@ if [ ! -d results_genome_scan ]; then
 fi
 cd data_parameters/
 
-nb_chromosomes=$(cat "nb_chromosomes.txt")    
-nb_snp_hap=$(cat "nb_snp_hap.txt")    
+nb_chromosomes=$(cat "nb_chromosomes.txt")
+nb_snp_hap=$(cat "nb_snp_hap.txt")
 kernel_index=$(cat "kernel_index.txt")
 
 modify_signif_level=false	# true or false (note lower case)
@@ -33,7 +33,7 @@ cp physical_map.txt			../results_genome_scan
 cp phased_genotypes.txt			../results_genome_scan
 cp kernel_index.txt			../results_genome_scan
 cp signif_level.txt			../results_genome_scan
- 
+
 cd ../programs/
 cp get_results_scans.R			../results_genome_scan
 cp plot_nb_hap_scans.R			../results_genome_scan
@@ -62,19 +62,19 @@ if [ "$kernel_index" -gt 1 ] ; then
 	if [ "$nb_snp_hap" -gt 1 ] ; then
 
 		for chromo_num_k in $(seq $nb_chromosomes -1 1)
-		do	
+		do
 			if [ -d results_chromo_num_$chromo_num_k ]; then
 				rm -rf results_chromo_num_$chromo_num_k/*
 			else
 				mkdir results_chromo_num_$chromo_num_k
-			fi			
+			fi
 			mv flanking_markers_of_tested_positions_in_kb_with_rlrt_value_on_chromosome_$chromo_num_k*		results_chromo_num_$chromo_num_k
-			mv flanking_markers_of_tested_positions_in_kb_with_significant_rlrt_value_on_chromosome_$chromo_num_k*	results_chromo_num_$chromo_num_k	
+			mv flanking_markers_of_tested_positions_in_kb_with_significant_rlrt_value_on_chromosome_$chromo_num_k*	results_chromo_num_$chromo_num_k
 			if ls significant_haplotypes_chromo_num_$chromo_num_k* 1> /dev/null 2>&1; then
 				mv significant_haplotypes_chromo_num_$chromo_num_k*						results_chromo_num_$chromo_num_k
 			fi
-			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k 
-			mv vect_nb_hap_window_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k 
+			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k
+			mv vect_nb_hap_window_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k
 			mv number_of_haplotypes_per_window_for_chromosome_$chromo_num_k*					results_chromo_num_$chromo_num_k
 			mv kernelized_haplotype_based_genome_scan_of_chromosome_$chromo_num_k*					results_chromo_num_$chromo_num_k
 		done
@@ -87,7 +87,7 @@ if [ "$kernel_index" -gt 1 ] ; then
 		mv number_of_haplotypes_per_window_for_complete_genome_scan*							results_all_chromosomes
 		mv kernelized_haplotype_based_genome_scan_for_*									results_all_chromosomes
 		mv flanking_markers_of_tested_positions_with_statistics*							results_all_chromosomes
-		
+
 	else
 
 		for chromo_num_k in $(seq $nb_chromosomes -1 1)
@@ -102,7 +102,7 @@ if [ "$kernel_index" -gt 1 ] ; then
 			if ls significant_snps_chromo_num_$chromo_num_k* 1> /dev/null 2>&1; then
 				mv significant_snps_chromo_num_$chromo_num_k*							results_chromo_num_$chromo_num_k
 			fi
-			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k 
+			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k
 			mv kernelized_gwas_of_chromosome_$chromo_num_k*								results_chromo_num_$chromo_num_k
 		done
 
@@ -110,7 +110,7 @@ if [ "$kernel_index" -gt 1 ] ; then
 			rm -rf results_all_chromosomes/*
 		else
 			mkdir results_all_chromosomes
-		fi                                              
+		fi
 		mv kernelized_gwas_for_*											results_all_chromosomes
 		mv markers_of_tested_positions_with_statistics.txt*								results_all_chromosomes
 		rm vect_nb_hap_window_chromo_num_*
@@ -118,7 +118,7 @@ if [ "$kernel_index" -gt 1 ] ; then
 	fi
 
  else
- 
+
 	if [ "$nb_snp_hap" -gt 1 ] ; then
 
 		for chromo_num_k in $(seq $nb_chromosomes -1 1)
@@ -133,8 +133,8 @@ if [ "$kernel_index" -gt 1 ] ; then
 			if ls significant_haplotypes_chromo_num_$chromo_num_k* 1> /dev/null 2>&1; then
 				mv significant_haplotypes_chromo_num_$chromo_num_k*						results_chromo_num_$chromo_num_k
 			fi
-			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k 
-			mv vect_nb_hap_window_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k 
+			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k
+			mv vect_nb_hap_window_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k
 			mv number_of_haplotypes_per_window_for_chromosome_$chromo_num_k*					results_chromo_num_$chromo_num_k
 			mv haplotype_based_genome_scan_of_chromosome_$chromo_num_k*						results_chromo_num_$chromo_num_k
 		done
@@ -162,7 +162,7 @@ if [ "$kernel_index" -gt 1 ] ; then
 			if ls significant_snps_chromo_num_$chromo_num_k* 1> /dev/null 2>&1; then
 				mv significant_snps_chromo_num_$chromo_num_k*							results_chromo_num_$chromo_num_k
 			fi
-			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k 
+			mv vect_rlrt_value_chromo_num_$chromo_num_k*								results_chromo_num_$chromo_num_k
 			mv gwas_of_chromosome_$chromo_num_k*									results_chromo_num_$chromo_num_k
 		done
 
@@ -170,14 +170,14 @@ if [ "$kernel_index" -gt 1 ] ; then
 			rm -rf results_all_chromosomes/*
 		else
 			mkdir results_all_chromosomes
-		fi                                              
+		fi
 		mv gwas_for_*													results_all_chromosomes
 		mv markers_of_tested_positions_with_statistics.txt*								results_all_chromosomes
 		rm vect_nb_hap_window_chromo_num_*
 
-	fi    
+	fi
 
-fi    
+fi
 clear
 
 rm *.R
diff --git a/khamix.sh b/khamix.sh
index 450748e..e5d949e 100755
--- a/khamix.sh
+++ b/khamix.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 #=======================================================================#
-#  kernelized haplotype-based mixed model association mapping (KHAMIX)  #										
+#  kernelized haplotype-based mixed model association mapping (KHAMIX)  #
 #=======================================================================#
 # source modules for R
 # source module_load_r.sh
@@ -9,11 +9,11 @@
 #1. setting haplotype size, in number of markers, and trait to be analyzed #
 #--------------------------------------------------------------------------#
 trait_name="LLGTH"
-nb_snp_hap=6			
+nb_snp_hap=6
 nb_chromosomes=12		# total number of chromosomes for the analyzed data set
-kernel_index=1			# 1 for VanRaden linear kernel and 2 for Gaussian kernel (i.e. RBF)		        
+kernel_index=1			# 1 for VanRaden linear kernel and 2 for Gaussian kernel (i.e. RBF)
 signif_level=0.01		# significance level for the restricted likelihood ratio test (RLRT)
-local_or_cluster=1		# 1 for local computation and 2 for parallelize computation on a cluster 
+local_or_cluster=2		# 1 for local computation and 2 for parallelize computation on a cluster
 
 echo "$trait_name" > trait_name.txt
 echo "$nb_snp_hap" > nb_snp_hap.txt
@@ -48,8 +48,8 @@ cp programs/compute_estimates_h0.R				estimates_h0/
 cd estimates_h0/
 	R -q --vanilla<get_data_trait_name.R
 	R -q --vanilla<get_data_incidence.R
-	R -q --vanilla<compute_k_matrix.R	
-	R -q --vanilla<compute_estimates_h0.R	
+	R -q --vanilla<compute_k_matrix.R
+	R -q --vanilla<compute_estimates_h0.R
 cd ../
 
 #-------------------------------------------------------------------------#
@@ -64,43 +64,43 @@ do
 	#3.1 creation of the directory for chromosome chromo_num_k to be analyzed #
 	#-------------------------------------------------------------------------#
 	mkdir genome_scan_chromo_num_$chromo_num_k
-	
+
 	# copy data into the directory for chromosome chromo_num_k
 	mv chromo_num_k.txt					genome_scan_chromo_num_$chromo_num_k
 	cp data_parameters/nb_snp_hap.txt			genome_scan_chromo_num_$chromo_num_k
 	cp data_parameters/nb_chromosomes.txt			genome_scan_chromo_num_$chromo_num_k
 	cp data_parameters/genotypes.txt			genome_scan_chromo_num_$chromo_num_k
 	cp data_parameters/phased_genotypes.txt			genome_scan_chromo_num_$chromo_num_k
-	cp data_parameters/physical_map.txt			genome_scan_chromo_num_$chromo_num_k 
-	
+	cp data_parameters/physical_map.txt			genome_scan_chromo_num_$chromo_num_k
+
 	# copy data and estimates for model under null hypothesis (h0) into directory for chromosome chromo_num_k
 	cp estimates_h0/phenotypes_trait_name.txt		genome_scan_chromo_num_$chromo_num_k
 	cp estimates_h0/x_matrix.txt				genome_scan_chromo_num_$chromo_num_k
 	cp estimates_h0/z_u_matrix.txt				genome_scan_chromo_num_$chromo_num_k
 	cp estimates_h0/k_matrix.txt				genome_scan_chromo_num_$chromo_num_k
 	cp estimates_h0/emmreml_h0				genome_scan_chromo_num_$chromo_num_k
-	
+
 	# copy programs into the directory for chromosome chromo_num_k
 	cp programs/get_data_chromo_num_k.R			genome_scan_chromo_num_$chromo_num_k
 	cp programs/ibs_haplotypes_window			genome_scan_chromo_num_$chromo_num_k
 	cp programs/compute_z_h_matrix				genome_scan_chromo_num_$chromo_num_k
 	cp programs/emmreml_rlrt.R				genome_scan_chromo_num_$chromo_num_k
-  	cp programs/scan_chromo_num_k.sh			genome_scan_chromo_num_$chromo_num_k  	
-  	
+  	cp programs/scan_chromo_num_k.sh			genome_scan_chromo_num_$chromo_num_k
+
 	# extract data associated to trait, fixed effects and compute Gram matrix (i.e. kernel matrix)
 	cd genome_scan_chromo_num_$chromo_num_k
 
-  	# perform genome scan by sliding window for chromosome $chromo_num_k 
+  	# perform genome scan by sliding window for chromosome $chromo_num_k
 	if [ "$local_or_cluster" -gt 1 ] ; then
 		# qsub -q normal.q -v scan_chromo_num_k.sh  # a cc2 queue
-		# sbatch scan_chromo_num_k.sh			
-		qsub -q workq scan_chromo_num_k.sh			
+		sbatch scan_chromo_num_k.sh
+		# qsub -q workq scan_chromo_num_k.sh
 	else
 		./scan_chromo_num_k.sh
 	fi
-   
+
 	# moving to the next directory "genome_scan_chromo_num_$chromo_num_k",
 	# i.e. moving up the directory tree
 	cd ../
-done  
+done
 
diff --git a/make_scripts_programs_executable.sh b/make_scripts_programs_executable.sh
index 01e3872..292cde4 100755
--- a/make_scripts_programs_executable.sh
+++ b/make_scripts_programs_executable.sh
@@ -2,7 +2,7 @@
 echo
 chmod u+rwx module_load_R.sh
 chmod u+rwx clean_scans.sh
-chmod u+rwx khammix.sh
+chmod u+rwx khamix.sh
 chmod u+rwx get_results_scans.sh
 chmod u+rwx programs/ibs_haplotypes_window
 chmod u+rwx programs/compute_z_h_matrix
diff --git a/programs/scan_chromo_num_k.sh b/programs/scan_chromo_num_k.sh
index e1b6118..0a70833 100755
--- a/programs/scan_chromo_num_k.sh
+++ b/programs/scan_chromo_num_k.sh
@@ -6,20 +6,20 @@ chromo_num_k=$(cat "chromo_num_k.txt")
 nb_snp_chromo_num_k=$(cat "nb_snp_chromo_num_k.txt")
 nb_snp_hap=$(cat "nb_snp_hap.txt")
 
-nb_scanned_positions=$(( nb_snp_chromo_num_k-	$((nb_snp_hap-1)) )) 
+nb_scanned_positions=$(( nb_snp_chromo_num_k-	$((nb_snp_hap-1)) ))
 
 # genome scan for chromosome $chromo_num_k
-for scanned_position in $( seq 1 1 $nb_scanned_positions )  
-do        	   
-	echo "$scanned_position">scanned_position.txt 
-	
+for scanned_position in $( seq 1 1 $nb_scanned_positions )
+do
+	echo "$scanned_position">scanned_position.txt
+
 	#compute ibs status of haplotypes
 	./ibs_haplotypes_window
 	./compute_z_h_matrix
-	  
+
 	# compute restricted likelihood ratio from emmreml estimated parameters
-	R -q --vanilla<emmreml_rlrt.R		  
+	R -q --vanilla<emmreml_rlrt.R
 	cat rlrt_value.txt>>vect_rlrt_value_chromo_num_$chromo_num_k.txt
 	cat nb_col_h_matrix.txt>>vect_nb_hap_window_chromo_num_$chromo_num_k.txt
-done 
+done
 # end of genome scan for chromosome $chromo_num_k