#!/usr/bin/perl

open(FO,">Annotations.cds");

open(FI,"Predictions.cds");
while($line=<FI>){
    chomp($line);
    @col=split(/\s+/,$line);
    $name="$col[0]";
    $length=0;$s=0;

    open(FA,"CreateDb.example.fa");
    while($lfa=<FA>){
	chomp($lfa);
	if(index($lfa,">")==0){
	    if($s==1){
		last;
	    }
	    $nim=substr($lfa,1,length($lfa)-1);
	    if($nim eq "$name"){
		$s=1;
		next;
	    }
	}
	if($s==1){
	    $lfa=~tr/[a-z]/[A-Z]/;
	    $lfa=~s/[^A-Z]//g;
	    $lin=length($lfa);
	    $length+=$lin;
	}
    }
    close FA;
    splice(@col,1,0,$length);
    print FO "@col\n";

}
close FI;

close FO;