fiddles with the GFF3 mRNA spans based on CDSes

change_mrna_gff3.pl

#!/usr/bin/env perl

my $inf = shift;

open IN, $inf;

my %cds;

# slurpy block
while (<IN>){
	chomp;
	my @F = split;
	if (/Parent=([^;]+)/){
		my $id = "$1";
		$cds{$id}->{start}||=$F[3];
		$cds{$id}->{stop}||=$F[4];

		$cds{$id}->{start}=$F[3] if $F[3] < $cds{$id}->{start};
		$cds{$id}->{stop}=$F[4]  if $F[4] > $cds{$id}->{stop};
	}
}
close IN;

# fixie block

# while (my ($k,$v)= eadch %cds){
#	print "funky "
# }


open IN, $inf;
while (<IN>){
	if (/ID=([^;\n]+)/){
	  	my @F=split;
		my ($newStart,$newStop) = ($cds{$1}->{start},$cds{$1}->{stop});
		my ($oldStart,$oldStop) = ($F[3],$F[4]);
		s/$oldStart/$newStart/;
		s/$oldStop/$newStop/;
	}
	print
}