gtf2gff3.pl: convert ensembl gtf to gff3 format, just for JBrowser

gtf2gff3.pl

#/usr/bin/perl -w

use strict;
use Data::Dumper;

## Written by [email protected]
## convert ensembl gtf to gff3 format, just for JBrowser

my ($gtf_f, $chr_list_f) = @ARGV; # ensembl gtf file, gtf from different source are different.

my %chr;
open IN,"$chr_list_f" || die $!;
while(<IN>){
	chomp;
	my @t = split /\t/;
	$chr{$t[0]} = $t[1];
}
close IN;

my %gtf;

&read_gtf($gtf_f, \%gtf, \%chr);

#print Dumper(\%gtf);

# output gff file
print "##gff-version 3\n";
foreach my $chr (sort keys %gtf){
	foreach my $gid (keys %{$gtf{$chr}}){
		# output the gene records
		my $attr = pop @{$gtf{$chr}{$gid}{'gene'}};
		print "####\n";
		print join "\t",@{$gtf{$chr}{$gid}{'gene'}};
		print "\tID=$gid\n";
		
		foreach my $tid (keys %{$gtf{$chr}{$gid}}){
			next if($tid eq "gene");
			# output transcript record
			$gtf{$chr}{$gid}{$tid}{'trans'}->[2] = "mRNA";
			my $attr_trans = pop @{$gtf{$chr}{$gid}{$tid}{'trans'}};
			my $trans_name = $1 if($attr_trans =~ /transcript_name "([^"]+)"/);
			print join "\t",@{$gtf{$chr}{$gid}{$tid}{'trans'}};
			print "\tID=$tid;Name=$trans_name;Parent=$gid";
			print "\n";

			# output CDS, exon, three_prime_UTR, five_prime_UTR
			my $flag = $gtf{$chr}{$gid}{$tid}{'flag'};
			my @flag_sorted = sort {$a->[3] <=> $b->[3]} @$flag;
			my $cds_seq = 0;
			foreach my $f (@flag_sorted){
				my $f_attr = pop(@$f);
				if($f->[2] eq "UTR" && $cds_seq == 0){
					if($f->[6] eq "+"){
						$f->[2] = "five_prime_UTR";
					}elsif($f->[6] eq "-"){
						$f->[2] = "three_prime_UTR";
					}
					print join "\t",@$f;
					print "\tParent=$tid;Name=$trans_name\n";
				}elsif($f->[2] eq "UTR" && $cds_seq == 1){
					if($f->[6] eq "-"){
						$f->[2] = "five_prime_UTR";
					}elsif($f->[6] eq "+"){
						$f->[2] = "three_prime_UTR";
					}
					print join "\t",@$f;
					print "\tParent=$tid;Name=$trans_name\n";
				}else{
					if($f->[2] eq "CDS"){
						$cds_seq = 1;
					}

					print join "\t",@$f;
					print "\tParent=$tid;Name=$trans_name\n";
				}
			}
		}
	}
}

# read in gtf file
sub read_gtf{
	my ($f, $gtf, $c) = @_;
	open IN,"$f" || die $!;
	while(<IN>){
		next if(/^#/);
		chomp;
		my @t = split /\t/;
		
		next unless($c->{$t[0]});
		my $chr = $c->{$t[0]};
		$t[0] = $chr;
		my $start = $t[3];
		my $end = $t[4];
		my $strand = $t[6];
		
		($t[3],$t[4]) = ($t[4],$t[3]) if($t[3]>$t[4]);
		
		my ($geneid,$transid) = ("","");
		$geneid = $1 if($t[8] =~ /gene_id "([^"]+)";/);
		$transid = $1 if($t[8] =~ /transcript_id "([^"]+)";/ && $t[2] ne "gene");
		
		if($t[2] eq "gene"){
			$gtf{$chr}{$geneid}{'gene'} = \@t;
		}elsif($t[2] eq "transcript"){
			$gtf{$chr}{$geneid}{$transid}{'trans'} = \@t;
		}else{
			push @{$gtf{$chr}{$geneid}{$transid}{'flag'}},\@t;
		}
	}
	close IN;
}