[maker-devel] Can maker select a gene model based on #algoritham predicted it

[Gowthaman Ramasamy]

Hi Carson,
Thanks for all the help during the long weekend, in spite of that long drive. I am still trying to imagine that.

I now have maker to consider our own prediction via pred_gff, and use augustus and gene mark (with our training model). And i was able to use altest and protein evidences. Maker happily picks one gene model when there is a overlap between three different predictions. But, when I look at the gff, it seems like it picks a gene model only when there is an est/protein evidence. It leaves out some genes even though, they are predicted by all three algorithms. Of course, keep_pred=1 helps to keep all the models. This kind of leads to over prediction. 

But, I am looking for something in between. And would like to know if that is possible?
1) Pick a gene model if it has an evidence from (est/prot etc...) irrespective of how many algorithms predicted it
2) In the absence of extrinsic evidence (est/prot etc), pick a gene model if that is predicted by at least two algorithms.

Or even simpler:
I have ab-initio predictions from three algorithms, Can I output, those genes that is supported by at least two of them. I care less about exactness of gene boundaries.

Thanks,
Gowthaman

PS: With my recent attempts, i learned couple things about maker/other associated tools that is not documented in gmod-maker wiki. Is it possible/ok if I add contents to it. I am okay with running it by you before making it public.