open (IN1,"<","$ARGV[0]");#gff3
#chr_001 Manual  gene    256     1182    .       +       .       ID=g18410;Name=TTHERM_00161861;UserNamed=Unnamed;TGDAnno=Unknow;info=hypothetical protein;
#chr_001 Manual  mRNA    256     1182    .       +       .       ID=g18410.t1;Parent=g18410;
#chr_001 Manual  five_prime_UTR  256     333     .       +       .       ID=g18410.t1.utr;Parent=g18410.t1;
#chr_001 Manual  CDS     334     342     .       +       .       ID=g18410.t1.cds;Parent=g18410.t1;
#chr_001 Manual  CDS     394     453     .       +       .       ID=g18410.t1.cds;Parent=g18410.t1;
#chr_001 Manual  CDS     505     855     .       +       .       ID=g18410.t1.cds;Parent=g18410.t1;
#chr_001 Manual  three_prime_UTR 856     1182    .       +       .       ID=g18410.t1.utr;Parent=g18410.t1;
open (IN2,"<","$ARGV[1]");#DESeq2
open (OUT1,">","$ARGV[2]");#normalized.outputfile
while (defined ($_=<IN1>)){
	if ($_=~/\s+gene\s+\d+\s+\d+\s+.+?ID=(g\d+);Name=(TTHERM_\d+);/){
		$hash{$1}=$2}
	elsif ($_=~/\s+five_prime_UTR\s+(\d+)\s+(\d+)\s+.+?ID=(g\d+)/){
		$tmp=($2-$1+1)/1000;
		$name=$hash{$3};
		$length{$name}+=$tmp;}
	elsif ($_=~/\s+CDS\s+(\d+)\s+(\d+)\s+.+?ID=(g\d+)/){
		$tmp=($2-$1+1)/1000;
                $name=$hash{$3};
                $length{$name}+=$tmp;}
	elsif ($_=~/\s+three_prime_UTR\s+(\d+)\s+(\d+)\s+.+?ID=(g\d+)/){
                $tmp=($2-$1+1)/1000;
                $name=$hash{$3};
                $length{$name}+=$tmp}
}
print OUT1 "GeneID\tIBD1-BRD-ave\tIBD1-KO-ave\tSB210-ave\tIBD1-BRD-1\tIBD1-BRD-2\tIBD1-BRD-3\tIBD1-KO-1\tIBD1-KO-2\tIBD1-KO-3\tSB210-1\tSB210-2\tSB210-3\n";
while (defined ($_=<IN2>)){
	if ($_=~/(TTHERM_\d+)\s+(.+?)\s+(.+?)\s+(.+?)\s+(.+?)\s+(.+?)\s+(.+?)\s+(.+?)\s+(.+?)\s+(.+)/){
		$name=$1;
		$BRD1=$2/$length{$name};
		$BRD2=$3/$length{$name};
		$BRD3=$4/$length{$name};
		$KO1=$5/$length{$name};
                $KO2=$6/$length{$name};
                $KO3=$7/$length{$name};
		$SB2101=$8/$length{$name};
                $SB2102=$9/$length{$name};
                $SB2103=$10/$length{$name};
		$BRD=($BRD1+$BRD2+$BRD3)/3;$KO=($KO1+$KO2+$KO3)/3;$SB210=($SB2101+$SB2102+$SB2103)/3;
		print OUT1 "$name\t$BRD\t$KO\t$SB210\t$BRD1\t$BRD2\t$BRD3\t$KO1\t$KO2\t$KO3\t$SB2101\t$SB2102\t$SB2103\n"}}