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Osteosarc 0.7.0

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@iskandr iskandr released this 25 Sep 03:15
· 33 commits to main since this release
v0.7.0
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Every source correction was re-checked against the reference genome and the website's own data, and the problems the check found are fixed.

python -m pip install --upgrade osteosarc==0.7.0

No correction only rewrites an equivalent form. Every allele was rebuilt on GRCh37 and GRCh38 reference sequence. Each allele fix corrects a different haplotype, replaces a placeholder (dup, not_reported), or fills in a missing allele. The one exception, transcript-DCHS2 adding a version to a valid accession, is fixed below.

Fixed

  • Tempus labels. The Tempus tumor carries all three variants seen only at T0 and none of the 35 seen only at T1. So the site's T1 labels on the Tempus files are probably wrong, not the timeline's T0 date. tempus-timepoint now says so, and a new flag, tempus-file-labels, marks the files.
  • provider-IPISRC044-T1-rna also fixes the site's read-count rows, which switched to UCLA on 2026-09-21.
  • transcript-DCHS2 fixes only the NM_1142552 typo, to the versionless form the site now uses, and shows as fixed upstream.
  • New accession fixes: transcript-COL4A2 (NM_001846.) and transcript-GTF3C5 (NM_00112283 → NM_001122823).
  • MAP2 keeps the site's read counts as an approximation. The site counts any large deletion at that spot, which in the T0 tumor exome is always the real change.
  • USH2A. The retired entry is a confirmed duplicate: its position is outside the gene. The kept entry's sequence context, which was taken from the typo position, is fixed.
  • Moved Tempus alleles drop sequence context taken from the wrong position.
  • fam157a-withdrawn-protein shows as fixed upstream where the site has the same note.
  • Summaries drop numbers that couldn't be reproduced.

Engine. An expected None now also matches a missing field. A correction's reported action comes from the correction itself.

Docs. The corrections page is rewritten in plain language.

On today's website snapshot: 35 corrections, 30 applied and 5 already fixed on the site, none stale. A 2026-09-18 snapshot applies all 35.

Validation:

  • CI passes on Python 3.9–3.13, including Varcode 7/9 consumer checks.
  • 255 tests pass against the built wheel in a clean virtualenv.
  • curation --strict passes on the live snapshot.
  • The affected documentation examples pass against live osteosarc.com.

PR #42 · Corrections · PyPI

https://claude.ai/code/session_01CcNHdiWgNhPGLmd4kDvG9G

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