deeptools_plotprofile

#!/bin/bash

if [[ -z $1 ]]; then
	echo "Usage: "
	echo -e "\t\$1: The bwfile (single mode) or '\$bwfile \$output_dir \$sample_label \$thread' for xargs multicore mode."
	echo -e "\t\$2: The output_dir."
	echo -e "\t\$3: The sample_label."
	echo -e "\t\$4: The thread for each single run."

	exit 100
fi

bwfile=$1
output_dir=$2
sample_label=$3
thread=$4
gtf=~/Genomes/GENCODE/Human/hg38/gtf/gencode.v40.annotation.gtf

# 2 mode
n=$(echo ${bwfile} | awk -F " |\t" '{print NF}')
if [[ $n -eq 4 ]]; then
	# multiple
	output_dir=$(echo ${bwfile} | cut -d " " -f2)
	sample_label=$(echo ${bwfile} | cut -d " " -f3)
	thread=$(echo ${bwfile} | cut -d " " -f4)
	bwfile=$(echo ${bwfile} | cut -d " " -f1)
	echo "multiple mode: $sample_label"
elif [[ $n -eq 1 ]]; then
	# single
	echo "single mode: $sample_label"
else
	echo "The \$1 is wrong, please check"
	exit 100
fi

# create the directory
mkdir -p ${output_dir}/{1.raw_data,2.data,3.pic}/{1.TSS,2.Body}

# TSS
if true; then
	output=${output_dir}/1.raw_data/1.TSS/${sample_label}_point_tss.gz
	mat=${output_dir}/2.data/1.TSS/${sample_label}_point_tss.mat
	pic=${output_dir}/3.pic/1.TSS/${sample_label}_point_tss.png
	computeMatrix reference-point \
		--scoreFileName ${bwfile} --regionsFileName ${gtf} \
		--outFileName ${output} \
		--samplesLabel ${sample_label} \
		--binSize 200 -a 2000 -b 2000 \
		--referencePoint TSS --averageTypeBins median \
		--numberOfProcessors ${thread} --skipZeros
	plotProfile -m ${output} \
		--outFileNameData ${mat} \
		-out ${pic}
fi

# body
if true; then
	output=${output_dir}/1.raw_data/2.Body/${sample_label}_body.gz
	mat=${output_dir}/2.data/2.Body/${sample_label}_body.mat
	pic=${output_dir}/3.pic/2.Body/${sample_label}_body.png
	computeMatrix scale-regions \
		--scoreFileName ${bwfile} --regionsFileName ${gtf} \
		--outFileName ${output} \
		--samplesLabel ${sample_label} \
		--binSize 200 -a 2000 -b 2000 -m 5000 \
		--averageTypeBins median \
		--numberOfProcessors ${thread} --skipZeros
	plotProfile -m ${output} \
		--outFileNameData ${mat} \
		-out ${pic}
fi