Is there a way to get the CDS structure for a given transcript?
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HGVS provides the following transcript information:
Example transcript: NM_001126049.1
"exon_structure": "89618918,89623194",
"relative structure": "[[1, 4277]]",
"tl_start_site": 951,
"tl_stop_site": 1487
I also want the corresponding CDS structure, just as we have the exon structure, something like:
"cds_structure": "89621708,89622244",
We were computing this as (first exon starting position) + (tl_start_site) and (last exon ending position + tl_stop_site) or opposite as in this case, the given that this transcript is on the reverse strand: 89623194 - 951 = 89,622,243 + 1 so the beginning of our CDS structure is: "cds_structure": "89621708,89622244",
The problem we hit doing it this way is that it doesn't account for partially aligning exons. Is there a straightforward way to grab this CDS structure information using the library that will take this into consideration? One out of the box idea I had was checking for the genomic position of C.1 (and C.*1 -1 ). This would at least get the start and stop correct but I'm not sure about all of the other positions.
Thanks!
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