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osteosarc 0.1.0

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@iskandr iskandr released this 19 Sep 00:06
· 83 commits to main since this release
v0.1.0
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First release of osteosarc: one verified data API for the public osteosarc.com dataset, shared by Varcode, Isovar, Topiary and Vaxrank.

python -m pip install 'osteosarc[reads]'
  • Pinned metadata snapshots that reopen offline, discovery of every bucket object, source-attributed sample claims, and variants and vaccines with their original annotations.
  • Header-checked indexed read extraction, VCF access, and a CLI.
  • 29 optional, evidence-backed source corrections in osteosarc/curation.py. They are re-checked against the live sources on every load, and osteosarc curation --strict reports drift.
  • A timeline of 787 dated events, and specimens linked to their files, browsable as ASCII charts or with the interactive osteosarc explore.
  • Files are stored in the shared OpenVax cache (objects/sha256/<sha256><suffixes> under OPENVAX_DATA_CACHE), the layout vaxrank also uses.

Documentation: https://iskandr.github.io/osteosarc/ · PyPI: https://pypi.org/project/osteosarc/0.1.0/

https://claude.ai/code/session_015FTcEX8deE5QQ9RospGFGJ

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