annotations_pipeline: gene_biotype vs gene_type

[jscaber]

Should the annotations pipeline be able to handle both gtfs with a gene_type and gene_biotype annotation? At the moment only gene_biotype is supported. Gene_type is ignored and the biotype is fetched from the source column instead.

At the moment the following code exists in gtf2gtf:
if "gene_biotype" not in gff.attributes: gff.setAttribute("gene_biotype", gff.source)

Should we be able to handle both formats or is this unlikely to bother anyone in the future?
ENCODE uses "gene_type".

[sebastian-luna-valero]

Hi @jscaber

Have you had a look at CGATOxford/CGATPipelines#323

[Acribbs]

I think this should be solved with the new pipeline. If im wrong please open it again.