Dataprovider - get canonical / MANE transcript

[davmlaw]

There is often the need for picking 1 transcript for a gene. This is often referred to as the canonical transcript, and nowadays (clinically) is usually the MANE transcript

It would be good to add a method to data provider to be able to retrieve the MANE transcript from a gene name

Transcripts could also have a field/flag on them saying whether they are MANE transcripts

Once we have the data provider API done, implementations like UTA or cdot could implement them

This is necessary to implement #517

Also came up as a request for #743

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[davmlaw]

The main question here is how to handle UTA implementation. It doesn't look like a modification to that will be available any time soon

I could make a shim around calls to UTA and implement MANE stuff by loading MANE.GRCh38.v1.4.summary.txt.gz - 1.1Mb

So you could either supply that file, or get a NotImplementedError thrown

I will have a crack at this when I get home (currently at a conference)

[andreasprlic]

This could be implemented somewhere around the get_tx_for_region method. Eg. as a second filter on top of the initial response, (only return tx_acs that are part of MANE transcripts).