feat: refactor hgvsTools and support c. translation
#366
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It would be nice, albeit out of scope here, if the generic |
jsstevenson
changed the title
c. translationc. translation
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@larrybabb can you pull in changes from |
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@korikuzma @jsstevenson @ahwagner could you please try to prioritize reviewing this PR? The primary purpose of it was to get support for the |
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@larrybabb I am in the middle of reviewing 😄 James is PTO today, but he did an initial review already |
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@larrybabb Great work! Overall, I like this change. I made some suggestions
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@larrybabb as Kori said, I'm out for at least today (which will probably entail some frantic catch-up once I'm back) but for the sake of pragmatism, we can assume my approval once Kori's additional notes above are addressed |
| 'refget_accession' (str): The accession ID of the reference genome. | ||
| 'start' (int): The start position of the allele. | ||
| 'end' (int): The end position of the allele. | ||
| literal_sequence' (str): The literal sequence for the allele. |
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| literal_sequence' (str): The literal sequence for the allele. | |
| 'literal_sequence' (str): The literal sequence for the allele. |
| sstate = models.LiteralSequenceExpression(sequence=ins_seq) | ||
| allele = models.Allele(location=location, state=sstate) | ||
| allele = self._post_process_imported_allele(allele, **kwargs) | ||
| # TODO: ask other devs if this should be down on all _from_... methods? |
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| # TODO: ask other devs if this should be down on all _from_... methods? |
Address #365
Begin refactoring the Translator logic to aggregate the functions and logic related to
hgvsand provide support forc.from and to translation. This should be step in the direction of re-thinking the organization of how the Translators are architected.