pirl-unc / hitlist / 25297452144
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coverage: 71.336% (+0.02%) from 71.315%
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v1.30.32: Curate Shapiro 2025 HAP1 KO panel from MCP supplements (#54) (#221)

Closes #54. The Shapiro 2025 paper's processed peptide tables (PMID
40113210, MCP) live as supplementary mmc6.csv attached to the
article — not in PRIDE PXD056426, which only carries RAW + search-
engine ZIPs. Europe PMC (PMC12090245) serves the bundle without
auth or rate limit.

Curation:
- 12 per-condition CSVs in hitlist/data/supplementary/
  (wildtype + 11 single-gene KOs: B2M, CALR, CANX, ERAP1, GANAB,
  IRF2, PDIA3, SPPL3, TAP1, TAP2, TAPBP). Each row is a peptide
  observed in ≥1 of 3 biological replicates, collapsed from
  mmc6.csv's 36 sample-density columns.
- 12 supplementary.yaml manifest entries (one per CSV) with
  per-CSV ``cell_name: "HAP1 <KO>"`` so the v1.30.30 sample
  resolver routes each CSV's peptides to the matching ms_sample
  in the existing pmid_overrides.yaml entry.
- ms_samples ``n_samples: 1 → 3`` (3 biological replicates per
  condition) and refreshed the study note with the data-source
  pointer.

Per-condition peptide counts (now in obs.parquet):
  wildtype       18,624
  CALR KO        17,331
  CANX KO        16,252
  SPPL3 KO       14,906
  GANAB KO       11,449
  ERAP1 KO        9,283
  TAP1 KO         9,048
  PDIA3 KO        7,237
  IRF2 KO         5,314
  TAPBP KO        4,498
  TAP2 KO         3,193
  B2M KO            520

Total 117,655 newly resolved sample-level peptides. The B2M KO
near-zero count is biologically expected (B2M is required for
HLA-I surface expression).

Resolver tightening:

The v1.30.30 token-prefix scorer matched at common-prefix ≥3
chars regardless of completeness, so "tapasin" (in TAPBP KO's
perturbation field) prefix-matched "tap1" via the family root
"tap" — routing TAP1-KO obs to the TAPBP sample.

Updated rule: a token-prefix match qualifies only when one
token is a complete prefix of the other (≥3 chars), OR when
the common prefix is ≥4 chars. "ifn" still matches "ifng"
(complete prefix); "lymphoblast" sti... (continued)

3855 of 5404 relevant lines covered (71.34%)

0.71 hits per line

Coverage Regressions

Lines Coverage ∆ File
32
81.61
 0.09% export.py
Jobs
ID Job ID Ran Files Coverage
1 25297452144.1 27
71.34
 GitHub Action Run
Source Files on build 25297452144