SACGF / SACGF/variantgrid

HGVS Search that also includes gene symbol

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#452 4 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
HGVS search
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

Searched for "IDH2: NM_002168.3:c.419G>A"

View details in Rollbar: [https://rollbar.com/jimmy.andrews/VariantGrid/items/3101/](https://rollbar.com/jimmy.andrews/VariantGrid/items/3101/)

```
Traceback (most recent call last):
File "/data/variantgrid/variantopedia/search.py", line 359, in search_within
build_results = get_results_func(self.search_string,
File "/data/variantgrid/variantopedia/search.py", line 511, in search_hgvs
raise original_error # cleaning didn't work don't tell anyone
File "/data/variantgrid/variantopedia/search.py", line 492, in search_hgvs
if fixed_hgvs := HGVSMatcher.fix_swapped_gene_transcript(hgvs_string):
File "/data/variantgrid/genes/hgvs.py", line 535, in fix_swapped_gene_transcript
hgvs = HGVSName(hgvs_name)
File "/usr/local/lib/python3.8/dist-packages/pyhgvs/__init__.py", line 758, in __init__
self.parse(name)
File "/usr/local/lib/python3.8/dist-packages/pyhgvs/__init__.py", line 772, in parse
self.parse_allele(allele)
File "/usr/local/lib/python3.8/dist-packages/pyhgvs/__init__.py", line 859, in parse_allele
raise NotImplementedError("unknown kind: %s" % allele)
NotImplementedError: unknown kind: NM_002168.3:c.419G>ATraceback (most recent call last):
File "/data/variantgrid/variantopedia/search.py", line 500, in search_hgvs
variant_tuple = hgvs_matcher.get_variant_tuple(hgvs_string)
File "/data/variantgrid/genes/hgvs.py", line 392, in get_variant_tuple
variant_tuple = pyhgvs.parse_hgvs_name(lookup_hgvs_name, self.genome_build.genome_fasta.fasta,
File "/usr/local/lib/python3.8/dist-packages/pyhgvs/__init__.py", line 1382, in parse_hgvs_name
hgvs = HGVSName(hgvs_name)
File "/usr/local/lib/python3.8/dist-packages/pyhgvs/__init__.py", line 758, in __init__
self.parse(name)
File "/usr/local/lib/python3.8/dist-packages/pyhgvs/__init__.py", line 772, in parse
self.parse_allele(allele)
File "/usr/local/lib/python3.8/dist-packages/pyhgvs/__init__.py", line 859, in parse_allele
raise NotImplementedError("unknown kind: %s" % allele)
NotImplementedError: unknown kind: NM_002168.3:c.419G>A
```

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