Weird formatting of column 9 in gff3 lift-over

[TDDB-limagrain]

Hi @Kuanhao-Chao ,
I was able to properly run Lifton using one plant reference genome and a new one to annotate from the same species.
The command was:

lifton -g ref.gff3 -o liftover.gff3 -P ref.pep.fasta -copies -sc 0.95 newgenome.fasta refgenome.fasta

The resulting lift-over file looks quite good for many gene models, but for some of them, there is a duplication in the exon names. See below the example a gene with 8 exons in the reference genome.

newgenomeLG00	LiftOn	gene	279378	285818	.	+	.	ID=newgenomeLG00g00180;Name=newgenomeLG00g00180;source=Liftoff
newgenomeLG00	LiftOn	mRNA	279378	285818	.	+	.	ID=newgenomeLG00g00180.1;Parent=newgenomeLG00g00180;Name=newgenomeLG00g00180.1;mutation=frameshift;protein_identity=0.999;dna_identity=1.000;status=LiftOn_chaining_anewgenomeLGorithm
newgenomeLG00	LiftOn	exon	279378	280607	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:001;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	exon	281921	282006	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:001;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	exon	282142	282299	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:001;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	exon	282401	283715	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:001;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	exon	283912	284186	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:001;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	exon	284379	284585	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:001;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	exon	284668	284824	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:001;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	exon	285132	285818	.	+	.	ID=_newgenomeLG00_1g00140.1:exon:008;Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	280585	280607	.	+	0	Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	281921	282006	.	+	1	Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	282142	282299	.	+	2	Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	282401	283715	.	+	0	Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	283912	284186	.	+	2	Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	284379	284585	.	+	0	Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	284668	284824	.	+	0	Parent=newgenomeLG00g00180.1
newgenomeLG00	LiftOn	CDS	285132	285430	.	+	2	Parent=newgenomeLG00g00180.1

In addition to that, would it be possible to automatically add a unique ID to each CDS? this can be mandatory for downstream applications.

Thanks!