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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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can we create an entire gene model if more than a single isoform when creating from a canvas track, currently it errors #2418

Open nathandunn opened 4 years ago

nathandunn commented 4 years ago
nathandunn commented 4 years ago

can probalby use volvox data

nathandunn commented 4 years ago

With the volvox data, we have this here:

image

Oddly, it only adds the first part of it up there, which is less than ideal. i.e., it actually has the entire gene model with mRNA's:

image

nathandunn commented 4 years ago

The problem is that the model should be sending 3 mRNA's. However, in this case it is sending one mRNA (the gene) and calling the sub-mRNA's the exons:

image

{"track":"ctgA","features":[{"location":{"fmin":1049,"fmax":9000,"strand":1},"type":{"cv":{"name":"sequence"},"name":"mRNA"},"name":"EDEN","children":[{"location":{"fmin":1049,"fmax":9000,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"},"children":[{"location":{"fmin":1200,"fmax":7608,"strand":1},"type":{"cv":{"name":"sequence"},"name":"CDS"}},{"location":{"fmin":1200,"fmax":1500,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":6999,"fmax":7608,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":2999,"fmax":3902,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":4999,"fmax":5500,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}}]},{"location":{"fmin":1049,"fmax":9000,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"},"children":[{"location":{"fmin":1200,"fmax":7608,"strand":1},"type":{"cv":{"name":"sequence"},"name":"CDS"}},{"location":{"fmin":1200,"fmax":1500,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":6999,"fmax":7608,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":4999,"fmax":5500,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}}]},{"location":{"fmin":1299,"fmax":9000,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"},"children":[{"location":{"fmin":3300,"fmax":7600,"strand":1},"type":{"cv":{"name":"sequence"},"name":"CDS"}},{"location":{"fmin":6999,"fmax":7600,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":3300,"fmax":3902,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}},{"location":{"fmin":4999,"fmax":5500,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}}]}]}],"operation":"add_transcript","clientToken":"781822412741028269425028547"}
nathandunn commented 4 years ago

I think its implemented this way, because if the top-level is a gene, we just create a simple CDS.

What we should be doing instead is say that if the top-level is a gene, and it has sub-features that are mRNA, it should add the mRNA features.

nathandunn commented 4 years ago

I think that this would make more sense to implement as part of a more comprehensive solution. The workaround at the moment is simply to use HTML Features or provide top-level mRNA, which should be the default anyway.

Longer-term, I would like to support this, however.