Keep introns

[christopher-holt]

Altered functionality of RNA.introns() to keep the introns annotated in the augustus.hints.gff3 file instead of dynamically generating introns

[jorvis]

So I get that the updates to biothings.py here supports your need from the augustus output, but it strips export of features from any other source but Augustus. Are you up for modifying that intron export behavior if ['introns'] is defined, else keep the version which derives them instead?

[christopher-holt]

The reason I chose to pull directly from Augustus was that I was having issues with naming the introns (eg "g1.t1.intron1"), following the same patterns as the exon/CDS names instead of using the uuid4. I can try and modify the intron export behaviour but I'm not sure how far I will get

[christopher-holt]

It would probably be easier to fix the naming issue but I haven't found a way yet

[christopher-holt]

Hi Josh, I kept the dynamic intron generation but I formatted the intron names to follow the same pattern as the exons (g1.t1.intron1). I know it is a bit hard coded but I wasn't sure of a better way to achieve this format (b88e02b)