pirl-unc / hitlist / 27280246711

Build # 27280246711

Build Type

push

github

Committed by web-flow

Commit Message

v1.36.0: pmhc --by-gene rollup + named gene sets (CTA) (#324)

Two additions for per-gene / per-panel analysis:

--by-gene: one row per gene with n_observations / n_unique_peptides /
n_references / n_samples, plus a panel total (observations summed, peptides /
refs / samples UNIONed across genes). Attributes each observation to its
gene(s) via the long-form peptide_mappings, so a peptide multi-mapping to
several genes counts for each. Honors --species / --source-context.

--gene-set NAME: expands a named gene set (data/gene_sets.yaml) into the --gene
filter. Ships the CTA panel (cancer-testis antigens: MAGE-A/B/C, GAGE, XAGE,
SSX, PRAME, CTAG, SPANX, + others; MAGE-D excluded as broadly expressed).
--list-gene-sets prints what's available.

So 'hitlist pmhc --gene-set CTA --by-gene' answers 'observations / unique
peptides per CTA' in one command.

Coverage Stats

5473 of 6845 relevant lines covered (79.96%)

0.8 hits per line

Source File

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