Label ref seqs #22
Label ref seqs #22
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| else: | ||
| allele.location.sequenceReference.label = hgvs_string.split(":")[0] |
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There will always be a colon in the hgvs string right? Just making sure we don't ever raise a key error down below.
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There should always be a colon in the post-mapped hgvs string, as long as the hgvs string was created by the function _create_post_mapped_hgvs_strings.
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We are assuming that there's no colon in the transcript or chromosome name, though. I think that's a safe assumption, but if that assumption were to be wrong, then the post-mapped variant would not be created for the variant, and you're right that the associated error for that variant would be a KeyError.
| # TODO address this hardcoding, and if we keep it, this should be a score set mapping error message | ||
| # if metadata.urn == "urn:mavedb:00000072-a-1": | ||
| # msg = f"No RefSeq accession is available for {metadata.urn}." | ||
| # if not silent: | ||
| # click.echo(msg) | ||
| # _logger.warning(msg) | ||
| # return None | ||
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Will this raise a mapping error now?
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This score set raises a mapping error without the hardcoding now. This was addressed in the first release of the mapper for mavedb, but I hadn't removed the commented out code.
Add human-readable sequence labels to post-mapped VRS output.
Remove commented-out hardcoding, since the mapper handles this score set correctly without hardcoding.