Commit cf20c27c authored by Marine Bergot's avatar Marine Bergot

Upload New File

parent c4e2680f
#!/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
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