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Author: XuanCao-CX

bdg_to_binarize.sh

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+#!/bin/bash
+
+
+usage() {
+    echo "Usage: make binary file from the bedgraph file. "
+    echo " 	Normalized value: bins per million mapped reads (BPM) , depth (nFrag or ReadsInTss) and cell_num (per 100 cells)."
+    echo "	bed_to_bdg.sh [-i bedgraph] [-o out_dir] [-f cutoff]  [-m mark] [-t cell_type/cluster]"
+    echo "		      [-s bin_size] [-c chrom_size]"
+    echo "Description:"
+    echo "	-i bedgraph, the input bedgraph file path."
+    echo "    	-o out_dir, the output dir name."
+    echo "    	-f cutoff, used to binarye."
+    echo "    	-m mark, the ChIPseq mark name, example H3K27me3."
+    echo "    	-t cell_type / cluster name,"
+    echo "    	-s bin_size, should the same with bedgraph file. Default:500."
+    echo "    	-c chrom_size, the chroms size file."
+    exit -1
+}
+ 
+
+
+bin_size=500
+
+while getopts 'h:i:o:f:m:t:s:c:' opts
+do
+	case $opts in
+		i) bdg="$OPTARG";;
+		o) out_dir="$OPTARG";;
+		f) cutoff="$OPTARG";;
+		m) mark="$OPTARG";;
+		t) cell_type="$OPTARG";;
+		s) bin_size="$OPTARG";;
+		c) chrom_size="$OPTARG";;
+		h) usage;;
+        	?) usage;;
+    	esac
+done
+
+
+function binary_one_chr(){
+	# $1 input_bdg, should the same with bin_size
+	# $2 out, out file path
+	# $3 mark
+	# $4 cell type / cluster
+	# $5 chr
+	# $6 chrom_size file
+	# $7 bin_size
+	bdg=$1;out=$2;mark=$3;cell_type=$4;chr=$5;chrom_size=$6;bin_size=$7
+	grep -w $chr $chrom_size|bedtools makewindows -g - -w $bin_size|\
+	bedtools intersect -a - -b $bdg -wao|\
+	awk -v cut=$cutoff '{if ($5 != -1 && $7 >cut){v=1}else{v=0};print v}'|\
+	sed "1i$cell_type\t$chr\n$mark" > $out
+}
+
+if [ ! -d "$out_dir" ]
+then
+	mkdir -p $out_dir
+fi
+
+chroms=(`cut -f 1 $chrom_size|grep -v random|grep -v chrUn|grep -v hap|grep -v chrM|grep -v chrY|tr '\n' ' '`)
+
+for chr in ${chroms[@]}
+do
+	o=${out_dir}/${cell_type}_${chr}"_binary.txt" 
+	binary_one_chr $bdg $o $mark $cell_type $chr $chrom_size $bin_size &
+done
+wait
+