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We show a list of transcripts to select from on the classification and variant page.
Some of these will fail as they are not valid c.HGVS coordinates (off transcript etc)
They may have worked in PyH…
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In order to keep organized as things scale, we need to structure the packages a little differently.
Each online resource should have an interface class:
* **NCBI Variation Services**: This is a …
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Add SPDIs at the top of all of the variant pages, and in the disambiguation boxes on the left
![Image](https://github.com/user-attachments/assets/8fed2373-fc46-4ff5-82e1-ee6367266ed8)
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I am currently getting a parser error when using the `o.` genomic DNA identifier (from https://varnomen.hgvs.org/bg-material/refseq/). The error can be reproduced with the following code:
```python
…
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When converting c. HGVS from cDNA to genome coordinates, VEP appears to not take into account alignment gaps, where the cDNA has insertions/deletions vs the reference sequence.
Submission example:
…
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We currently use [parsley](http://parsley.readthedocs.io/en/latest/) to parse HGVS expressions. Parsley was last released in 2015. The most recent commit on github is 2017. The project appears to be d…
reece updated
3 months ago
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Example from EMMAA covid model:
WARNING: [2021-08-17 14:29:41] indra.assemblers.pybel.assembler - Node should not have variants: bp(MESH:D019895 ! Transposases), [{'kind': 'hgvs', 'hgvs': 'p.?'}]
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The hgvs library has a built in (text-based) visualization, which allows to build a view of the context of a variant with the alignment between the transcript and the reference genome. It can create r…
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### Background:
SPDI (Sequence Position Deletion Insertion) nomenclature and HGVS (Human Genome Variation Society) nomenclature are two standards that when used correctly, can uniquely identify seq…
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The hgvs dataprovider has way too much implicit behavior, which creates surprises for users and developers.
Drop all implicit behavior. hdp.connect() should require a URL.
Then, put all of the …
reece updated
3 months ago