Closed Peter-J-Freeman closed 1 year ago
The variant description chr12:112037477G>A
does validate and reveals that the variant lies in the 5' UTR of coding transcripts of the ATXN2 gene.
Using the GRCh37 HGVS-compliant description (NC_000012.11:g.112037477G>A)
as a template, the variant description chr12:112037477G>GAAA
can be re-written as NC_000012.11:g.112037478_112037479insAAA
and this does validate without errors.
This suggests that the original version of the variant description (chr12:112037477G>GAAA)
is not being correctly parsed prior to validation.
Great analysis. Thanks @leicray
Adding this variant as well variant = 'NM_002468.4:c.855_894delinsATCTG'
Traceback (most recent call last):
File "/local/py3Repos/vv_hgvs/vvhgvs/parser.py", line 138, in rule_fxn
return self._grammar(s).__getattr__(rule_name)()
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/parsley.py", line 98, in invokeRule
raise err
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/parsley.py", line 85, in invokeRule
ret, err = self._grammar.apply(name, *args)
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/ometa/runtime.py", line 462, in apply
val, err = self._apply(r, ruleName, args)
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/ometa/runtime.py", line 495, in _apply
[rule(), self.input])
File "/pymeta_generated_code/pymeta_grammar__Grammar.py", line 38, in rule_hgvs_variant
_G_or_13, lastError = self._or([_G_or_1, _G_or_3, _G_or_5, _G_or_7, _G_or_9, _G_or_11])
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/ometa/runtime.py", line 604, in _or
raise joinErrors(errors)
During handling of the above exception (
NM_002468.5:c.*-36_*3delinsATCTG
^
Parse error at line 1, column 15: expected a digit. trail: [digit num def_c_pos c_pos def_c_interval c_interval c_posedit c_variant hgvs_variant]
), another exception occurred:
File "/local/py3Repos/variantValidator/VariantValidator/modules/vvMixinCore.py", line 750, in validate
toskip = mappers.transcripts_to_gene(my_variant, self, select_transcripts_dict_plus_version)
File "/local/py3Repos/variantValidator/VariantValidator/modules/mappers.py", line 709, in transcripts_to_gene
hgvs_updated = validator.hp.parse_hgvs_variant(hgvs_updated)
File "/local/py3Repos/vv_hgvs/vvhgvs/parser.py", line 141, in rule_fxn
s=s, exc=exc, reason=exc.formatReason()))
During handling of the above exception (NM_002468.5:c.*-36_*3delinsATCTG: char 15: expected a digit), another exception occurred:
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/django/core/handlers/exception.py", line 47, in inner
response = get_response(request)
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/django/core/handlers/base.py", line 181, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/local/VVweb/web/views.py", line 144, in validate
output = tasks.validate(variant, genome, select_transcripts, validator=validator)
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/celery/local.py", line 191, in __call__
return self._get_current_object()(*a, **kw)
File "/local/miniconda3/envs/vvweb/lib/python3.6/site-packages/celery/app/task.py", line 391, in __call__
return self.run(*args, **kwargs)
File "/local/VVweb/web/tasks.py", line 20, in validate
output = validator.validate(variant, genome, transcripts)
File "/local/py3Repos/variantValidator/VariantValidator/modules/vvMixinCore.py", line 1442, in validate
raise fn.VariantValidatorError('Validation error')
Describe the bug GRCh37:12:112037477:G:GAAA
chr12:112037477G>GAAA
chr12:112037475GGG>GGGAAA
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