Export column - c_hgvs_compat

[davmlaw]

https://app.testiny.io/VG/testcases/tcf/81/tc/173/edit

• Change c_hgvs_full to chgvs_compat
• Change MVLs to use that
• Convert inv to delins
• Also convert LRG to NM_ and Ensembl to RefSeq? (or link/raise another issue for that)

[davmlaw]

We should be able to turn it from INV to delisn pretty easily in Biocommons code:

Out[81]: VariantCoordinate(chrom='1', start=1637084, end=1637084, ref='TCCCAG', alt='CTGGGA')
In [86]: hgvs_variant = matcher.variant_coordinate_to_hgvs_variant(vc)
In [87]: hgvs_variant
Out[87]: NC_000001.10:g.1637084_1637089inv

In [88]: hgvs_variant._sequence_variant
Out[88]: SequenceVariant(ac=NC_000001.10, type=g, posedit=1637084_1637089inv, gene=None)

In [89]: sv = hgvs_variant._sequence_variant

In [90]: sv.posedit.edit.ref
Out[90]: 'TCCCAG'

In [91]: ref = sv.posedit.edit.ref

In [92]: sv.posedit.edit = NARefAlt(ref=ref, alt=reverse_complement(ref))

In [93]: sv
Out[93]: SequenceVariant(ac=NC_000001.10, type=g, posedit=1637084_1637089delinsCTGGGA, gene=None)

In [94]: str(sv)
Out[94]: 'NC_000001.10:g.1637084_1637089delinsCTGGGA'

[EmmaTudini]

@davmlaw Has this been done? Is it ready for testing? We'll likely need this before the prod deploy

[davmlaw]

No this is still in progress

[davmlaw]

Request for Ensembl / LRG is done in https://github.com/SACGF/variantgrid_private/issues/2541

[davmlaw]

Integration is export only, so just need to get MVL to pull this column rather than the old one

[davmlaw]

Needs Shariant test

Tes
t by creating classification against eg NM_000127.3(EXT1):c.1315_1320inv (can just use random coords to make an inv)

To to classification -> export -> Select MVL - ensure that column comes out without an inv (eg c.1315_1320delTCACGTinsACGTGA)

[TheMadBug]

To confirm, I believe this is only relevant when we switch to biocommons and then refresh all the imported allele infos, as pyhgvs does not resolve things to inv.

As we are looking to switch to biocommons after the next deploy (all Shariant environments still have HGVS_DEFAULT_METHOD="pyhvs")

@davmlaw can you confirm that this is only relevant for biocommons - I found no inv's in the MVL currently.

[davmlaw]

Yes, only biocommons has "inv"

[davmlaw]

Tested vg test (make sure to classify against a RefSeq transcript so it appears in MVL)

MVL c_nomen came out as c.1315_1320delTCACGTinsACGTGA

[TheMadBug]

I've updated the resolved info admin screen to be able to search on c.HGVS/c.HGVS compatible as well as show if there's a different in the column.

So we can now search for "inv" https://test.shariant.org.au/admin/classification/resolvedvariantinfo/?q=inv and see that the cononical c.HGVS has inv, but the compatible version is del/ins

[davmlaw]

@TheMadBug - I did a test case on this, it was only when I finished that I saw you had already done it.

Should we have the convention that the test case is in the top description?

I did mine in Classification/Download/MVL - https://app.testiny.io/VG/testcases/tcf/89/tc/184/edit while yours is in Variant

I think yours is "code centric" - I can see why you put it there because of the models. While I was trying to arrange it from a user perspective as the place it matters is the export. We should work out which way we want to put things?

[TheMadBug]

Oops, I had put the test case at the end of the first comment, not at the end of the description where I normally do it.
That said, going forward, I'm happy to put test case links at the top of descriptions.

I've also added the label Has Test Case to relevant projects and renamed the variantgrid label has_testiny_test_case to Has Test Case for consistency.

So I have tried to reduced redundancy as well as make comprehensive test cases of functionality. A good example is showing the ACMG/Horak codes summaries, they appear both in the classification listing and the CSV download.
https://app.testiny.io/VG/testcases/tcf/88/tc/181/edit I have 5 test steps - sort order, not showing neutral strengths, showing override strengths, point based vs non-point based criteria.

In the test cases that cover the CSV download and the classification listing, I have done a subset of that testing, but reference the comprehensive test plan.
Lastly the whole process caused me to make the admin screen more useful be able to identiy the relevant data.