implement method to identify/describe transcripts regions for variant

[reece]

Originally reported by: Reece Hart (Bitbucket: reece, GitHub: reece)

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e.g., given c. variant, return something like "exon 3", "intron 2", "exon 1..2", "5' UTR", {'exons': [1,2,3]}.

This needs a spec before implementing. The spec should provide a data model for representing the spans, then a way to turn that into something humans would read.

Considerations:

• comparison overlaps v. contained in

• output type: need human and machine usable (e.g., "exon 5..6" and {exon_start: 5, exon_end: 6})

• Perhaps this is better implemented after refining the hdp interface types?

• general function (e.g., which_region(var) -> dict) v. specific output (which_exon(var) -> int)? v. boolean (is_3p_UTR?) v. SO?

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• Bitbucket: https://bitbucket.org/biocommons/hgvs/issue/242

[Melodeiro]

Thats would be useful information!

Our use case is information about all regions (exons introns and UTRs), which intersects with variant, so maybe something like that would work:

{
    "exons": [1,2,3],
    "introns": [1,2]
}

We just need the whole information about the regions, by specific transcript of a variant.

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