feat!: add chromosome lookup to sequence reference utils#67
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jsstevenson merged 6 commits into0.2.0from Oct 27, 2025
Merged
feat!: add chromosome lookup to sequence reference utils#67jsstevenson merged 6 commits into0.2.0from
jsstevenson merged 6 commits into0.2.0from
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korikuzma
approved these changes
Oct 24, 2025
src/agct/seqref_registry.py
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| REFGET_ID_LOOKUP = {v: k for k, v in REFGET_ID_INFO.items()} | ||
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| _ERROR_PATTERN = re.compile(r"^SQ\.[0-9A-Za-z_\\-]{32}$") |
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We may consider renaming this to refget ac pattern (or something similar). Error pattern may be a little misleading
jsstevenson
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Oct 29, 2025
I just realized that you need to also know the chromosome name for your refget accession ID to do liftover, so I just moved stuff around in that module so both assembly and chromosome are returned.
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I just realized that you need to also know the chromosome name for your refget accession ID to do liftover, so I just moved stuff around in that module so both assembly and chromosome are returned.
I'm really hoping that I'm not messing up the refget/sequence reference terminology.