Edit protein sequence given HGVS.p

[Dario Beraldi]

Hello,

As per title, I need to edit a protein sequence according to a HGVS.p tag.  For example:

>ENSP00000454338
FPIEAGDSRGLAAAPESQDSPEAVATEHNPVSGPCRASISPGRFVAALDATA

Given:

ENSP00000454338.1:p.Ala37Thr

Return the input with Ala at position 37 changed to Thr:

>ENSP00000454338
FPIEAGDSRGLAAAPESQDSPEAVATEHNPVSGPCRTSISPGRFVAALDATA 

I came across the HGVS package and I'm wondering whether it could be used for this task. 

This is what I have so far but then I'm sort of stuck. Any help much appreciated!

import hgvs.parser

import hgvs.dataproviders.uta

import hgvs.assemblymapper

hgvsparser = hgvs.parser.Parser()

var = hgvsparser.parse_hgvs_variant('ENSP00000454338.1:p.Ala37Thr')

hdp = hgvs.dataproviders.uta.connect()

vm = hgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh38', alt_aln_method='splign')

 

Dario

[Reece Hart]

Hi Dario-

Sorry, this query was lost during my vacation.

The hgvs package doesn't have a way to generate the sequence that results from applying a variant. Sorry.

Please consider adding an issue if you'd like to see this implemented.

-Reece

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