make gene name sanitation optional #1084
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DriesSchaumont
requested changes
Oct 17, 2025
DriesSchaumont
requested changes
Oct 17, 2025
DriesSchaumont
requested changes
Oct 31, 2025
src/utils/set_var_index.py
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| # then an eleven digit number, optionally followed by .version_number | ||
| ensembl_pattern = re.compile(r"^(ENS.*\d{11})(?:\.\d+)?$") | ||
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| return [ |
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Would it be possible to use the index as input here and use index.to_series().str.startswith()
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Series.str.startswith.html
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Can we rule out that there are no genes that start with ENS?
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I think you can inverse the boolean mask returned by startswith using ~
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I meant https://pandas.pydata.org/docs/reference/api/pandas.Series.str.match.html, sorry about that ^^
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All good, it's adjusted now!
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Changelog
Make gene name sanitation optional:
recommended for removing versions from ensembleid's (e.g. ENSMUSG00000017167.6), but not for gene names with splice variants (e.g. AL627309.1)
Note: #1083 needs to be merged first
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Closes #xxxx (Replace xxxx with the GitHub issue number)
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Proposed changes are described in the CHANGELOG.md
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