Parse transcript allele to protein

Question

[roalva1]

Hello,

I have somthing like NM_000023.2:c.488dupG and I would like to parse it to protein, for example for NM_000016.5:c.127G>A the result would be p.Glu43Lys, would you know if there is any way to do it? I have 2000 to be done, so I should automatize it.

Thanks

[Titus]

Hi, Do you have only NM_000016.5:c.127G>A line by line in a file ?

Best

[roalva1]

I have a lot of different annotations, bwlow you can see an example of some: NM_000016.4:c.999_1011dupTAGAATGAGTTAC NM_000023.2:c.488dupG NM_000027.3:c.199_200delGA NM_000033.3:c.1489-6delC NM_000033.3:c.1581C>A NM_000033.3:c.1586_1588delGTG NM_000033.3:c.2T>A NM_000033.3:c.494delG NM_000033.3:c.707G>A NM_000033.3:c.757C>G

So I would need them in the protein format, like for example: NM_000016.5:c.127G>A p.Glu43Lys

Answer 1

[roalva1]

I know how to do it, whit this library: https://hgvs.readthedocs.io/en/latest/index.html