BB_PslMap~

#!/bin/bash

#######--Arguments--#######
help_info(){
	echo "usage:"
	echo "sh Mar23_PslPipeline.sh in.bed chrom.size over.chain out.prefix covergae_needed"
	echo "chrom.size is in the path /data/tongji2/InputForRunBT/ChromSize/"
	echo "over.chain is in the path /data/tongji2/InputForRunBT/LiftOver/"
}


if [ $# -lt 4 ];then
	help_info
	exit 1
fi

path_chrom=/data/tongji2/Annotation/ChromSize/
path_chain=/data/tongji2/Annotation/Chain/

###Run###
pre1=${1##*/}
pre2=${4##*/}
RN=${RANDOM}${RANDOM}${RANDOM}

if [ ! "${1##*.}" == "psl" ];then
	bedToPsl ${path_chrom}${2} ${1} temp_${pre1}.${RN}.psl
	pslMap -chainMapFile -swapMap temp_${pre1}.${RN}.psl ${path_chain}${3} ${4}.psl
	rm temp_${pre1}.${RN}.psl 
else
	pslMap -chainMapFile -swapMap ${1} ${path_chain}${3} ${4}.psl
fi

sort -k10,10 -k1,1nr ${4}.psl | awk '!a[$10]++' | awk -v ide=${5} '{FS="\t";OFS="\t"} {if($1/$11>ide){print $14,$16,$17,$10,$1/$11,$9}}' > ${4}.bed
sort -k10,10 -k1,1nr ${4}.psl | awk '!a[$10]++' > ${4}_temp.${RN}.psl && mv ${4}_temp.${RN}.psl ${4}.psl