Support for circular genomic identifiers

[mbiokyle29]

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:

from hgvs.easy import parse

# parse a variant from a plasmid using the circular genome
parse('plasmid:o.10A>G')
---------------------------------------------------------------------------
ParseError                                Traceback (most recent call last)
~/Dev/project/.venv/lib/python3.7/site-packages/hgvs/parser.py in rule_fxn(s)
    124                 try:
--> 125                     return self._grammar(s).__getattr__(rule_name)()
    126                 except ometa.runtime.ParseError as exc:

~/Dev/project/.venv/lib/python3.7/site-packages/parsley.py in invokeRule(*args, **kwargs)
     97                                      [["message", "expected EOF"]], err.trail)
---> 98             raise err
     99         return invokeRule

~/Dev/project/.venv/lib/python3.7/site-packages/parsley.py in invokeRule(*args, **kwargs)
     84             try:
---> 85                 ret, err = self._grammar.apply(name, *args)
     86             except ParseError as e:

~/Dev/project/.venv/lib/python3.7/site-packages/ometa/runtime.py in apply(self, ruleName, *args)
    461         if r is not None:
--> 462             val, err = self._apply(r, ruleName, args)
    463             return val, err

~/Dev/project/.venv/lib/python3.7/site-packages/ometa/runtime.py in _apply(self, rule, ruleName, args)
    494                 memoRec = self.input.setMemo(ruleName,
--> 495                                          [rule(), self.input])
    496             except ParseError as e:

/pymeta_generated_code/pymeta_grammar__Grammar.py in rule_hgvs_variant(self)
     37                 return (_G_apply_12, self.currentError)
---> 38             _G_or_13, lastError = self._or([_G_or_1, _G_or_3, _G_or_5, _G_or_7, _G_or_9, _G_or_11])
     39             self.considerError(lastError, 'hgvs_variant')

~/Dev/project/.venv/lib/python3.7/site-packages/ometa/runtime.py in _or(self, fns)
    603                 self.input = m
--> 604         raise joinErrors(errors)
    605

ParseError:
plasmid:o.10A>G
        ^
Parse error at line 1, column 8: expected one of 'c', 'g', 'm', 'n', 'p', or 'r'. trail: [p_variant hgvs_variant]


During handling of the above exception, another exception occurred:

HGVSParseError                            Traceback (most recent call last)
~/Dev/project/.venv/lib/python3.7/site-packages/hgvs/shell.py in <module>
----> 1 parse('plasmid:o.10A>G')

~/Dev/project/.venv/lib/python3.7/site-packages/hgvs/parser.py in parse(self, v)
    105
    106         """
--> 107         return self.parse_hgvs_variant(v)
    108
    109     def _expose_rule_functions(self, expose_all_rules=False):

~/Dev/project/.venv/lib/python3.7/site-packages/hgvs/parser.py in rule_fxn(s)
    126                 except ometa.runtime.ParseError as exc:
    127                     raise HGVSParseError(
--> 128                         "{s}: char {exc.position}: {reason}".format(s=s, exc=exc, reason=exc.formatReason())
    129                     )
    130

HGVSParseError: plasmid:o.10A>G: char 8: expected one of 'c', 'g', 'm', 'n', 'p', or 'r'

Seems like o. is not supported by the package. This is not a huge deal, but thought it was worth opening an issue. I'd be interested in providing a PR assuming I could get a little bit of guidance on the changes required. Seems like at a bare minimum I would need too:

• Update this regex: https://github.com/biocommons/hgvs/blob/main/src/hgvs/parser.py#L135
• Add expanded rules to https://github.com/biocommons/hgvs/blob/main/src/hgvs/_data/hgvs.pymeta for all the o cases

I am guessing there are other things that I am not aware of. Either way thanks for all the hard work on this package. It has been great to work with, the shell and .easy module are both great!

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[reece]

This issue was closed by stalebot. It has been reopened to give more time for community review. See biocommons coding guidelines for stale issue and pull request policies. This resurrection is expected to be a one-time event.

[github-actions]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.