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scripts_CNV/launch_pipeline_get_genes.sh

+#!/bin/bash
+
+
+TAD_file=$1
+echo $(pwd)
+mkdir -p $(pwd)/Analyses_genes
+mkdir -p $(pwd)/Analyses_genes/split_files
+mkdir -p $(pwd)/Analyses_genes/TADs_genes
+mkdir -p $(pwd)/Analyses_genes/TADs_sort
+mkdir -p $(pwd)/Analyses_genes/TADs_list_genes
+
+PATH_SCRIPT="/work/gad/shared/analyse/HiC/scripts"
+
+
+
+#split file with significatives TADs
+echo "split"
+
+echo split -dl 1 --additional-suffix=.bed $TAD_file $(pwd)/Analyses_genes/split_files/TAD
+
+#intersect with genes file
+echo "intersect"
+
+#for i in $(pwd)/Analyses_genes/split_files/*.bed; do bedtools intersect -b $i -a $(pwd)/Homo_sapiens.GRCh38.108_correct.bed -wo > $(pwd)/Analyses_genes/TADs_genes/$(basename $i .bed)_genes.bed; done
+
+#remove transcripts
+echo "transcript"
+
+#for i in $(pwd)/Analyses_genes/TADs_genes/*_genes.bed; do awk -F"\t" '!_[$4]++' $i > $(pwd)/Analyses_genes/TADs_sort/$(basename $i _genes.bed)_genes_sort.bed; done
+
+#get genes list
+echo "genes list"
+
+#for i in $(pwd)/Analyses_genes/TADs_sort/*.bed; do python $PATH_SCRIPT/get_genes_list.py $i $(pwd)/Analyses_genes/TADs_list_genes/$(basename $i _genes_sort.bed)_list_genes.txt; done
+
+#remove "
+#for i in $(pwd)/Analyses_genes/TADs_list_genes/*_list_genes.txt; do  sed -i 's/"//g' $i; done
+
+#get counts by genes
+#changer les pwd dedans
+echo "genes counts"
+
+#sh $PATH_SCRIPT/get_expr.sh $(pwd)/Analyses_genes/TADs_list_genes
+
+#plot R
+echo "plot"
+#1. remove empty genes
+#sh $PATH_SCRIPT/remove_empty_gene.sh $(pwd)/Analyses_genes/TADs_list_genes
+
+#2. reverse tab for R
+#sh $PATH_SCRIPT/launch_reverse_gene.sh $(pwd)/Analyses_genes/TADs_list_genes
+
+#3. plot
+
+sh $PATH_SCRIPT/launch_plot.sh $(pwd)/Analyses_genes/TADs_list_genes