Cufflinks FTP to Agustus hints GFF conversion (exon|intron|ep)

cufflinks2hints.pl

#!/usr/bin/env perl
#
# convert cufflinks GTF into a Augustus hintfile
#
# seq source ep|exon|intron start stop score +/- phase grp=ID; src=E

my %transcripts;

while(<>){
	next unless /Cufflinks\s+exon.*transcript_id/;
	s/"//g;
	chomp;
	my @c = split;
	push @{$transcripts{$c[11]}},{seq=>$c[0],name => $c[11],start => $c[3],stop => $c[4],strand => $c[6]};
}

while(my($k,$v)=each %transcripts){
	my @exons = sort {$a->{start} <=> $b->{stop}} @$v; # get them in the correct order ... just in case
	for(my $i=0;$i<scalar(@exons);$i++){
		my $ex=$exons[$i];

                unless($i == 0){
			my %intron = %$ex;
			$intron{start}=$exons[$i-1]->{stop}+1;
			$intron{stop} =$ex->{start}-1;
			print_gff(\%intron,'intron');
		}

		if($i == 0 || $i==scalar(@exons)-1){
			print_gff($ex,'ep');
		}
		else{
			print_gff($ex,'exon');
		}
	}
}

sub print_gff{
	my ($e,$source)=@_;
	printf "%s\tCufflinks\t$source\t%d\t%d\t.\t%s\t.\tgrp=%ssrc=W\n",$e->{seq},$e->{start},$e->{stop},$e->{strand},$e->{name}; 
}