CDS features do not have ID=

[nextgenusfs]

Looks like you are explicitly not writing IDs for CDS features? Why?? This goes against the GFF3 spec, CDS from the same mRNA feature should have the same ID.

LiftOn/lifton/liftoff/write_new_gff.py

Lines 100 to 113 in e07f41a

	def make_gff_line(attr_dict, feature):
	if feature.featuretype != "CDS":
	attributes_str = "ID=" + attr_dict["ID"][0] + ";" #make ID the first printed attribute
	else:
	attributes_str = ""
	for attr in attr_dict:
	if attr != "copy_id":
	value_str = ""
	for value in attr_dict[attr]:
	value_str += value + ","
	if attr != "ID":
	attributes_str += (attr + "=" + value_str[:-1] + ";")
	return feature.seqid + "\t" + feature.source + "\t" + feature.featuretype + "\t" + str(feature.start) + \
	"\t" + str(feature.end) + "\t" + "." + "\t" + feature.strand + "\t" + feature.frame + "\t" + attributes_str[:-1]

original

chrXIV  SGD     gene    51907   52431   .       -       .       ID=YNL310C;Name=ZIM17;Alias=HEP1,FMP28,ZIM17,TIM15;Product=Protein co-chaperone with a zinc finger motif;
chrXIV  SGD     mRNA    51907   52431   .       -       .       ID=YNL310C-T1;Parent=YNL310C;Product=Protein co-chaperone with a zinc finger motif;Alias=HEP1,FMP28,ZIM17,TIM15;Ontology_term=GO:0005739,GO:0005759,GO:0006457,GO:0006986,GO:0007005,GO:0030150,GO:0050821,GO:0051087;DBxref=SGD:S000005254;Note=Protein co-chaperone with a zinc finger motif, essential for protein import into mitochondria, may act with Pam18p to facilitate recognition and folding of imported proteins by Ssc1p (mtHSP70) in the mitochondrial matrix, required for the maintenance of Ssc1p solubility and assists in the functional interaction of Ssc1p with substrate proteins;
chrXIV  SGD     exon    51907   52431   .       -       .       ID=YNL310C-T1.exon1;Parent=YNL310C-T1;
chrXIV  SGD     CDS     51907   52431   .       -       0       ID=YNL310C-P1;Parent=YNL310C-T1;

lifton transfer

chrXIV	LiftOn	gene	74355	74879	.	-	.	ID=YNL310C;Name=ZIM17;Alias=HEP1,FMP28,ZIM17,TIM15;Product=Protein co-chaperone with a zinc finger motif;source=Liftoff
chrXIV	LiftOn	mRNA	74355	74879	.	-	.	ID=YNL310C-T1;Parent=YNL310C;Product=Protein co-chaperone with a zinc finger motif;Alias=HEP1,FMP28,ZIM17,TIM15;Ontology_term=GO:0005739,GO:0005759,GO:0006457,GO:0006986,GO:0007005,GO:0030150,GO:0050821,GO:0051087;DBxref=SGD:S000005254;Note=Protein co-chaperone with a zinc finger motif, essential for protein import into mitochondria, may act with Pam18p to facilitate recognition and folding of imported proteins by Ssc1p (mtHSP70) in the mitochondrial matrix, required for the maintenance of Ssc1p solubility and assists in the functional interaction of Ssc1p with substrate proteins;protein_identity=1.000;dna_identity=1.000;status=Liftoff
chrXIV	LiftOn	exon	74355	74879	.	-	.	ID=YNL310C-T1.exon1;Parent=YNL310C-T1
chrXIV	LiftOn	CDS	74355	74879	.	-	0	Parent=YNL310C-T1