Convert JGI gtf-like annotation file to GTF2.2 format

jgi2gtf.pl

#!/usr/bin/perl -w
use strict;
use warnings;

=head1
Author: [email protected]

This script converts a JGI gtf-like file:

scaffold_1	JGI	exon	46078	46218	.	+	.	name "gw.1.597.1"; transcriptId 65742
scaffold_1	JGI	CDS	46078	46218	.	+	0	name "gw.1.597.1"; proteinId 65742; exonNumber 1
scaffold_1	JGI	exon	46093	46218	.	+	.	name "gw.1.23.1"; transcriptId 6905
scaffold_1	JGI	CDS	46093	46218	.	+	0	name "gw.1.23.1"; proteinId 6905; exonNumber 1
scaffold_1	JGI	exon	48713	48808	.	-	.	name "gw.1.11.1"; transcriptId 1718
scaffold_1	JGI	CDS	48713	48808	.	-	0	name "gw.1.11.1"; proteinId 1718; exonNumber 6
scaffold_1	JGI	exon	51025	51074	.	-	.	name "gw.1.11.1"; transcriptId 1718
scaffold_1	JGI	CDS	51025	51074	.	-	0	name "gw.1.11.1"; proteinId 1718; exonNumber 5
scaffold_1	JGI	exon	51139	51229	.	-	.	name "gw.1.11.1"; transcriptId 1718
scaffold_1	JGI	CDS	51139	51229	.	-	2	name "gw.1.11.1"; proteinId 1718; exonNumber 4
scaffold_1	JGI	exon	51307	51381	.	-	.	name "gw.1.11.1"; transcriptId 1718
scaffold_1	JGI	CDS	51307	51381	.	-	0	name "gw.1.11.1"; proteinId 1718; exonNumber 3
scaffold_1	JGI	exon	52291	52379	.	-	.	name "gw.1.11.1"; transcriptId 1718
scaffold_1	JGI	CDS	52291	52379	.	-	0	name "gw.1.11.1"; proteinId 1718; exonNumber 2
scaffold_1	JGI	exon	52754	52955	.	-	.	name "gw.1.11.1"; transcriptId 1718
scaffold_1	JGI	CDS	52754	52955	.	-	2	name "gw.1.11.1"; proteinId 1718; exonNumber 1

To GTF2.2 (parseable by cufflinks):

scaffold_488	JGI	exon	2243	2367	.	-	.	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "1"; exon_id "fgenesh1_pg.scaffold_488000001.1";
scaffold_488	JGI	CDS	2243	2367	.	-	0	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "1"; exon_id "fgenesh1_pg.scaffold_488000001.1";
scaffold_488	JGI	exon	2746	3001	.	-	.	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "2"; exon_id "fgenesh1_pg.scaffold_488000001.2";
scaffold_488	JGI	CDS	2746	3001	.	-	1	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "2"; exon_id "fgenesh1_pg.scaffold_488000001.2";
scaffold_488	JGI	exon	3652	3853	.	-	.	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "3"; exon_id "fgenesh1_pg.scaffold_488000001.3";
scaffold_488	JGI	CDS	3652	3853	.	-	2	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "3"; exon_id "fgenesh1_pg.scaffold_488000001.3";
scaffold_488	JGI	exon	4866	4986	.	-	.	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "4"; exon_id "fgenesh1_pg.scaffold_488000001.4";
scaffold_488	JGI	CDS	4866	4986	.	-	0	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "4"; exon_id "fgenesh1_pg.scaffold_488000001.4";
scaffold_488	JGI	exon	5366	5621	.	-	.	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "5"; exon_id "fgenesh1_pg.scaffold_488000001.5";
scaffold_488	JGI	CDS	5366	5621	.	-	1	gene_id "fgenesh1_pg.scaffold_488000001"; transcript_id "fgenesh1_pg.scaffold_488000001"; exon_number "5"; exon_id "fgenesh1_pg.scaffold_488000001.5";
=cut

while(<>){
  my ($seqid,$src,$type,$start,$end,$score,$strand,$frame,$lastcol) = split(/\t/,$_);
  next unless $type eq 'CDS' || $type eq 'exon';

  my ($geneid,$transcriptid,$exonnumber);
  if( $lastcol =~ /(?:name|gene_id)\s+\"([^\"]+)\";/ ) {
    $geneid = $1;
  }

  if( $lastcol =~ /proteinId\s+(\d+)/ ) {
    $transcriptid = "$1";
  }
  if( $lastcol =~ /transcriptId\s+(\d+)/ ) {
    $transcriptid = "$1";
  }
  if( $lastcol =~ /exonNumber\s+(\d+)/ ) {
    $exonnumber = "$1";
  }
  print join("\t",$seqid,$src,$type,$start,$end,$score,$strand,$frame);
  print "\tgene_id \"$geneid\"\; transcript_id \"$transcriptid\"\;";
  if($exonnumber){
    print " exon_number \"$exonnumber\"\; exon_id \"$transcriptid\.$exonnumber\"\;";
  }
  print "\n";
}