Parsing repeat expansions
nh13 opened this issue · 1 comments
nh13 commented
I am getting errors parsing examples from repeat expansions. I see there's a Repeat
class in edit.py
, so I am clearly missing something (i.e. probably PEBKAC).
>>> p.parse("NC_000014.8:g.101179660TG[14]")
Traceback (most recent call last):
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/hgvs/parser.py", line 131, in rule_fxn
return self._grammar(s).__getattr__(rule_name)()
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/parsley.py", line 98, in invokeRule
raise err
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/ometa/runtime.py", line 554, in many
v, _ = fn()
File "/pymeta_generated_code/pymeta_grammar__Grammar.py", line 843, in _G_many_226
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/ometa/runtime.py", line 495, in _apply
[rule(), self.input])
File "/pymeta_generated_code/pymeta_grammar__Grammar.py", line 2668, in rule_dna
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/ometa/runtime.py", line 495, in _apply
[rule(), self.input])
File "/pymeta_generated_code/pymeta_grammar__Grammar.py", line 2683, in rule_dna_iupac
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/ometa/runtime.py", line 649, in pred
raise e
ometa.runtime.ParseError:
NC_000014.8:g.101179660TG[14]
^
Parse error at line 1, column 25: expected the character '='. trail: [dna_iupac dna dna_ident dna_edit g_posedit g_variant hgvs_variant]`
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/hgvs/parser.py", line 113, in parse
return self.parse_hgvs_variant(v)
File "/Users/nhomer/miniconda3/envs/hgvs/lib/python3.10/site-packages/hgvs/parser.py", line 133, in rule_fxn
raise HGVSParseError("{s}: char {exc.position}: {reason}".format(
hgvs.exceptions.HGVSParseError: NC_000014.8:g.101179660TG[14]: char 25: expected the character '='
I tried some of the other examples: LRG_763t1:c.53AGC[23]