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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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How to get protein annotation for a input genomic position #244

Closed damianosmel closed 3 years ago

damianosmel commented 3 years ago

Dear developers,

Thank you for creating this tool! I have used it already to automate some refinements of PVS1 evidence criterion, following Tayouen et al. 2018 work.

However, there are some steps that I need to know the annotation of the protein (product) for the input variant genomic position. In the docs there is no explanation for (an available) protein module.

So I would like to ask you, if there is a way on how to retrieve protein feature of a region that is the translation of an input genomic variant position? If there is such way may you please give a short of an example using pyensembl?

LuukHenk commented 3 years ago

I found a way to access protein sequences using the ensembl_id: data = EnsemblRelease() protein_ids = data.protein_ids() data.protein_sequence(protein_ids[0])

julia326 commented 3 years ago

Hi @damianosmel , sorry for the epic delay on this but glad to hear this tool is useful! We have a related tool for predicting the coding effect of a variant called Varcode, and you can use it like this:

from pyensembl import EnsemblRelease
from varcode import Variant

ensembl_grch38 = EnsemblRelease(95, species='human')
Variant(contig=4, start=1807189, ref='C', alt='G', ensembl=ensembl_grch38).effects()

Let me know if that doesn't answer your question though.

damianosmel commented 3 years ago

I found a way to access protein sequences using the ensembl_id: data = EnsemblRelease() protein_ids = data.protein_ids() data.protein_sequence(protein_ids[0])

Thank you @LuukHenk! I got similar logic by reading the pyensembl docs.

damianosmel commented 3 years ago

Hi @damianosmel , sorry for the epic delay on this but glad to hear this tool is useful! We have a related tool for predicting the coding effect of a variant called Varcode, and you can use it like this:

from pyensembl import EnsemblRelease
from varcode import Variant

ensembl_grch38 = EnsemblRelease(95, species='human')
Variant(contig=4, start=1807189, ref='C', alt='G', ensembl=ensembl_grch38).effects()

Let me know if that doesn't answer your question though.

Thank you for detailed answer @julia326. Varcode seems also a very helpful contribution, thanks to all the developers! To me, by a quick look on its repository, seems as an alternative to VeP or ANNOVAR so I will check out this functionality.

As I have made this issue more like a "how2", I will close this issue. Thank you!