fix the braker GTF, so it can be used with htsseq

fix_braker_gtf.pl

#!/usr/bin/env perl

while (<>){
	chomp;
	@F=split(/\s\s+/);
	if ($F[2] eq 'gene'){
		my $t = "gene_id \"$F[-1]\";";
		$F[-1]=$t;
	}elsif($F[2] eq 'transcript'){
		my $t="transcript_id \"$F[-1]\";";
		$F[-1]=~/(g\d+)\.t\d+/;
		$t.=" gene_id \"$1\";";
		$F[-1]=$t;
	}
	print join "\t",@F;
	print "\n";
}