Infer genes in gff3 files

[FabianJetzinger]

Hello, thank you for creating and maintaining this software!

I've recently come across a gff3 file (specifically, this one: https://sweetpotato.uga.edu/download_v3/NSP306_trifida_v3.hc.gene_models.gff3.zip) that has exon and mRNA entries with parent attributes, but lacked the gene entries. From what I understand, gffutils does not directly offer an option to infer genes for gff3 files.

While I've seen descriptions of gff3 formats without mRNA and gene entries (like https://www.ensembl.org/info/website/upload/gff3.html or https://gmod.org/wiki/GFF3#GFF3_Format), what is different about the aforementioned file is that it's missing those entries yet still contains the Parent attributes.

If this is a common dialect, it would be great to have native support for parsing it. If I've missed or misunderstood any existing option to achieve this, I apologize. While I've seen similar discussions in the issues here, I'm not sure if those solutions (e.g. manually reformatting and forcing it to parse as gtf) would be the recommended approach here.

Best regards,
Fabian Jetzinger

[FabianJetzinger]

Additionally, the link to the GFF format specification in the gffutils documentation (http://www.sanger.ac.uk/resources/software/gff/spec.htm) seems to no longer work correctly and now redirects me to the Sanger Tools Directory.