Update CNV_Analyses.slurm

Codes/CNV_Analyses.slurm

 #!/bin/bash
 #SBATCH --job-name=CNVs
-#SBATCH --output=/shared/home/righettin/Analyses/slurm_outputs/CNVs.out
-#SBATCH --error=/shared/home/righettin/Analyses/slurm_outputs/CNVs.error
+#SBATCH --output=Analyses/slurm_outputs/CNVs.out
+#SBATCH --error=Analyses/slurm_outputs/CNVs.error
 #SBATCH --cpus-per-task=48
 #SBATCH --nodes=1
 
 # Define paths
-root_dir="/shared/home/righettin/Analyses/CNV_estimates"
+root_dir="Analyses/CNV_estimates"
 analysis_dir="$root_dir/analysis"
-genes_id2name="/shared/home/righettin/Data/References/hg38/geneID2name_hg38_Apr24.tsv"
-paralogs="/shared/home/righettin/Data/References/hg38/paralogs_hg38_Apr24.txt"
+genes_id2name="Data/References/hg38/geneID2name_hg38_Apr24.tsv"
+paralogs="Data/References/hg38/paralogs_hg38_Apr24.txt"
 
 # 1) Concatenate all CNV estimates in a single file
 echo "1) Concatenating all CNV estimates in a single file:"
@@ -35,12 +35,12 @@ echo "Decimal places removed from the fifth column of $output_file."
 # 3) Compute Gene Matrix
 echo "3) Computing Gene Matrix for all genomes:"
 
-python3 /shared/home/righettin/Scripts/CNV_scripts/computeGeneMatrix.py -t $output_file -d $genes_id2name -p $paralogs > $analysis_dir/AllGenomes.type.nobl.cnv.matrix.ALL.tsv
+python3 Scripts/CNV_scripts/computeGeneMatrix.py -t $output_file -d $genes_id2name -p $paralogs > $analysis_dir/AllGenomes.type.nobl.cnv.matrix.ALL.tsv
 
 echo "Gene Matrix for all genomes computed and saved as $analysis_dir/AllGenomes.type.nobl.cnv.matrix.ALL.tsv."
 echo "Since this contains all genes, it can be filtered to retain only genes that have a gain or a loss in at least one archaic genome compared to the human reference:"
 
-python /shared/home/righettin/Scripts/CNV_scripts/computeGeneMatrix.py -t $output_file -d $genes_id2name -p $paralogs |
+python Scripts/CNV_scripts/computeGeneMatrix.py -t $output_file -d $genes_id2name -p $paralogs |
 awk 'NR==1{print;next} {for(i=5;i<=NF;i++){ if($i/$4<0.5||$i/$4>1.5){print;next} }}' > $analysis_dir/AllGenomes.type.nobl.cnv.matrix.tsv
 
 echo "Results are in $analysis_dir/AllGenomes.type.nobl.cnv.matrix.tsv."