pirl-unc / hitlist / 24584006611
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coverage: 43.416%. Remained the same
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v1.8.9: Fix Trolle 2016 HeLa sHLA + split per-allele + rename n → n_samples (#66)

* v1.8.8: Split Trolle 2016 pooled 721.221 transfectants (#57)

PMID 26783342 ms_samples pooled 5 HLA-A/B mono-allelic 721.221
transfectants into a single sample. Split into per-transfectant
entries so each peptide joins to its single transfectant sample
rather than a 5-allele pooled row:

  721.221-HLA-A*01:01 (2,921 peptides)
  721.221-HLA-A*02:01 (4,296 peptides)
  721.221-HLA-A*24:02 (3,915 peptides)
  721.221-HLA-B*07:02 (3,284 peptides)
  721.221-HLA-B*51:01 (1,222 peptides)

All rows already had allele-specific mhc_restriction and were flagged
mono-allelic via the PMID-level mono_allelic_host: 721.221 override
(IEDB cell_name annotation "HeLa cells-Epithelial cell" is a known
misannotation corrected by the override). The split only improves
per-sample metadata consistency — no classification changes.

Closes #57.

* v1.8.9: Fix Trolle 2016 to HeLa sHLA + rename n → n_samples

The Trolle 2016 entry was wrong: paper used HeLa cells transfected with
VLDLr-tagged soluble HLA (sHLA), not 721.221 transfectants. Verified from
PMC4744552 Methods. IEDB's cell_name=HeLa / source_tissue=Uterine Cervix
annotations were correct all along; the prior YAML note claiming IEDB was
"WRONG" was itself wrong. Switched mono_allelic_host: "721.221" →
mono_allelic_method: "sHLA (VLDLr-tagged, secreted)" since mono-allelic
status comes from affinity purification of the tagged sHLA, not host HLA
knockout. Sample labels: "721.221-HLA-*" → "HeLa-sHLA-HLA-*".

Separately: renamed 427 ms_samples `n:` → `n_samples:` across the YAML,
updated the single reader in export.py, and added an AGENTS.md rule
forbidding bare `n` as a count field. A bare `n` is ambiguous (samples vs.
runs vs. replicates) and the suffix prevents silent miscounting.

1210 of 2787 relevant lines covered (43.42%)

0.43 hits per line

Jobs
ID Job ID Ran Files Coverage
1 24584006611.1 19
43.42
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Source Files on build 24584006611