Annotation parsing file output options

[mchibucos]

For the annotation parsing file, it would be helpful to add a few options for different output types. GFF3 and protein fasta files are already generated. I would like to see these nucleic acid file outputs, as well:

1. gene (full gene, including UTRs, start, stop, exons and introns).
2. coding sequence (CDS from start to stop that get translated into protein)
3. gene plus 1000 bases up and downstream of start and stop.

Thanks!
Marcus