PANTHER IBA family review

Family-level (PANTHER/PAINT) review of the IBA annotations on the 40 reviewed
S. pombe genes. Reviews the source of the IBAs — the phylogenetic
propagation — rather than re-judging gene by gene.

• extract_iba_propagation.py — reproducible extractor: for each IBA, resolves
  the ancestral PANTHER node, the seed genes, and the subfamilies of our gene
  and its seeds (from the cached interpro/panther/<FAM>/ tables); flags
  cross-subfamily and localization propagations and joins our curation action.
• iba_propagation.tsv — the resulting per-IBA table (regenerate with the script).
  Carries inline node-level (PAINT) columns joined from IBD.gaf:
  node_seed_count (the authoritative canonical seed count curated at the source
  node, vs. the few n_seeds echoed into the leaf), node_evidence
  (IBD/IRD/IKR), and node_loss. New flags: SINGLE_NODE_SEED (≤1 canonical
  seed — weak support), NODE_LOSS (an IRD/IKR loss at the source node), and
  NODE_NOT_IN_IBD.
• extract_node_annotations.py — pulls the PTN node-level (PAINT) annotations
  themselves from PANTHER's IBD.gaf (the IBD/IRD/IKR — plus a few IBA-on-node —
  layer that is the source of every IBA). For each ancestral node our genes
  derive from, it lists the full
  node annotation set with the canonical seed counts, marks loss (IRD/IKR NOT)
  annotations, and flags node annotations that did not propagate to our gene
  (propagated=false → candidate missing annotation or lineage loss).
• node_annotations.tsv — the resulting per-node-annotation table.
• extract_function_losses.py — flags families where a subfamily lost a
  function: pairs every PAINT loss (any NOT annotation — usually IRD/IKR,
  occasionally NOT|IBD) with its ancestral gain node
  (IBD), checks the loss is within a cached family's PTN node set, and attributes
  it to the family subfamilies whose members descend from the loss node
  (resolved from the leaf GAF + member tables). This is the strongest
  within-family neo-/sub-functionalization signal and a direct curation guard:
  do not propagate the ancestral function to members under the loss node.
• family_function_losses.tsv — per-(family, lost-GO) findings with
  ancestral_node, loss_node, gain_confirmed, and the affected
  subfamilies. (n_members_affected=0 means the loss is in an unsampled
  subfamily — the gain→loss pair is still confirmed.)
• prepare_loss_analysis.py — turns one loss finding into a ready-to-run input
  bundle for a bioinformatics agent to reconstruct the key-residue rationale
  (PANTHER never publishes which residues an IKR was based on — see the IKR note
  below). Emits YAML with seed_uniprot (where the function + its key residues
  are characterized), loss_clade (members predicted to have lost it), and
  retaining_clade (members that kept it). The agent fetches these sequences,
  aligns them, and compares the functional columns. Example:

bash uv run python projects/PANTHER_IBA_REVIEW/prepare_loss_analysis.py \ --family PTHR10443 --loss-node PTN000047776 --go GO:0016805

Note: loss_clade/retaining_clade are resolved from the reviewed member
tables + leaf GAF, so a finding with n_members_affected=0 yields an empty
loss_clade (the loss is in an unsampled subfamily); seeds are still provided.
Of the 296 IKR findings, 49 have ≥1 attributed reviewed member and are
immediately actionable.
- REVIEW.md — the written review and findings.

Regenerate:

uv run python projects/PANTHER_IBA_REVIEW/extract_iba_propagation.py
uv run python projects/PANTHER_IBA_REVIEW/extract_node_annotations.py
uv run python projects/PANTHER_IBA_REVIEW/extract_function_losses.py

The node-level source files (IBD.gaf, leaf GAF) are downloaded on demand into
a gitignored .cache/panther/ and are not committed. Per-family node slices can
be materialised under interpro/panther/<FAM>/<FAM>-paint.tsv with:

just fetch-panther-paint PTHR10177

Scope: the 151 IBAs in the 40 reviewed genes (38 PANTHER families, all cached
locally). Note the cross-subfamily flag is deliberately sensitive and
over-fires on broadly conserved functions — it is triage, not a verdict.