Repository navigation
Pfam review: 16 owner-classified rows, specificity notes, owner decisions Q6-Q8, R0 status for C. albicans - #73
Merged
Conversation
… for composite calls Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
…heet Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JXibAde2qW2uRZ4pShs1sW
…the open rows Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…sheet complete Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…tivated) Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…no family activated Notes follow the owner review of 2026-10-07 (16 rows) and the counts in docs/reports/2026-10-07-pfam-specificity-notes-draft.md. active stays no for all 15 families. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Owner sign-off 2026-10-07 after the specificity review (8 rows classified, 25 of 29 hits are glycoside hydrolase or fragment false hits removed by the signal_peptide condition; the 4 hits that pass are S. cerevisiae FLO1, FLO5, FLO9, FLO10). With PA14 active: S288C 4 hits, Af293 0. Status stays unvalidated. The shipped-table test now pins the signed-off set. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
What this adds
Follow-up to #72 (merged before these commits were pushed). 15 commits.
uncharacterised_true_member, PA14 8 arefalse_domain_hit. Sheet:docs/reports/data/sorting_hat/specificity/review_sheet_first_signoff.tsv, with PredGPI calls, Af293 ortholog columns,n_tm_mature, and a full Pfam-A scan of the open rows (open10.pfamA_scan.domtbl). Each row's note records the owner's reasoning and caveats.data/sorting_hat/family_table.tsv: threespecificity_noteedits (CFEM, PA14, Hydrophobin).activeisnofor all 15 families. Nothing is activated. The change is its own commit (8b1692b). Draft and consequences:docs/reports/2026-10-07-pfam-specificity-notes-draft.md.docs/paper/03decision 3 corrected (composite calls report a derived status) anddocs/paper/04updated.smoke, sensitivity 0.477 [0.356, 0.591]); report and handoff updated.Read before merging
active = yesis the owner's separate change, committed alone, per Plan 2.pfam_proposals.pyfrom table facts. The member lists are drafts. The notes state counts, not sensitivity or specificity.no_tmdoes not remove it).maindiffers from this branch only by the merge commit of Pfam proposals, CGD curation leads, owner decisions, per-call status spec (grilling session 2026-10-07) #72.Package tests: 683 passed, 7 skipped (shellcheck absent). Pre-commit (ruff, ruff-format) passes. No code changed except analysis scripts already in #72.
🤖 Generated with Claude Code