Conversation
bencap
left a comment
bencap
left a comment
There was a problem hiding this comment.
lgtm, just a couple questions I was curious about.
| else: | ||
| allele.location.sequenceReference.label = hgvs_string.split(":")[0] |
There was a problem hiding this comment.
There will always be a colon in the hgvs string right? Just making sure we don't ever raise a key error down below.
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
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 | ||
|
|
There was a problem hiding this comment.
Will this raise a mapping error now?
There was a problem hiding this comment.
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.
2 participants
Add human-readable sequence labels to post-mapped VRS output.
Remove commented-out hardcoding, since the mapper handles this score set correctly without hardcoding.