Variant view

[moedarrah]

What to show in the Variant View

[Fattigman]

Here is an image on what to show from the flask version:

[moedarrah]

The variant endpoint is not working

[talnor]

This is the same issue as https://github.com/genomic-medicine-sweden/docker-sc2reporter/issues/29?

[Fattigman]

It is indeed, I will close it then because of duplication

[Fattigman]

We need to clarify

• cDNA Change
• Codon change
• Protein change
• External link CoVariants

[Fattigman]

Codon change = Codons cDNA change = HGVSc Protein change = HGVSp

[Fattigman]

The last one is a bit more tricky. It looks like: External link CoVariant = https://covariants.org/variants/{ SYMBOL+':'+HGVSp} But it's constructed like:

It is parsed in the code like:

https://covariants.org/variants/{ covariants[v] }

covariants = {
        "S:A222V": "20A.EU1", "S:S477N": "20A.EU2", "S:N501Y": "S.N501", "S:E484K": "S.E484",
        "S:H69_V70del": "S.H69-", "S:N439K": "S.N439K", "S:Y453F": "S.Y453F", "S:S98F": "S.S98F",
        "S:L452R": "S.L452R", "S:D80Y": "S.D80Y", "S:A626S": "S.A626S", "S:V1122L": "S.V1122L",
        "S:Q677H": "S.Q677"
    }
var_show = v
if v == "S:H69_V70del":
        var_show = "S.H69-"

Here is the web site it uses https://covariants.org/variants if you want to investigate the how the urls are constructed. Maybe this should be done in the backend instead?

[moedarrah]

I agree it would be better to send it from the backend.

[Fattigman]

This is now done via backend at #162