pirl-unc / tsarina / 35369459462
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coverage: 76.811% (-0.7%) from 77.546%
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Surface excluded-but-clinical-target CTAs; accept flexible --hla/--cta syntax (#161)

* Surface excluded-but-clinical-target CTAs, and accept flexible --hla/--cta syntax

personalize() silently dropped a --cta gene that oncoref excludes from
the strict CTA set (e.g. CTAG2/LAGE-1, excluded for a low-level HPA
heart RNA signal but tracked as a known clinical target given the
NY-ESO-1-family therapeutic history) -- indistinguishable from a
typo'd gene name. Such a gene now appears under category="cta_flagged"
with the exclusion reason in a new flag_reason column, generated
directly from the protein sequence since it's excluded from both the
strict CTA gene-ID universe cta_exclusive_peptides() resolves against
and the "non-CTA" background that same function's exclusivity filter
subtracts (running that filter on a flagged gene would zero out its
own peptides against itself). A --cta gene that's neither a
recognized CTA nor a known clinical target now warns by name instead
of vanishing the same way.

New tsarina.gene_sets.CTA_clinical_target_gene_names/_ids alias
oncoref's existing cta_clinical_target_gene_names/_ids, matching every
other CTA_* alias already there.

--hla and --cta now accept comma- and/or space-separated entries,
quoted or not (nargs="+" collects unquoted multi-token input, then a
shared flatten_multi() splits each token on both commas and
whitespace). --hla additionally normalizes every allele through
mhcgnomes (tsarina.mhc.parse_mhc), so HLA-A0201 and A0201 resolve to
the same HLA-A*02:01 as the canonical form -- the '*' is a shell glob
character, so accepting a form without it means --hla never strictly
requires quoting.

Bumps 1.27.2 -> 1.28.0.

Claude-Session: https://claude.ai/code/session_017AfXtBXCu777PSx7RohGSp

* Decouple the --cta CLI wiring test from real CTA peptide generation

test_personalize_cta_accepts_unquoted_space_separated failed in CI
(all 4 Python versions) but passed locally -- the difference is a
cold environment w... (continued)

3097 of 4032 relevant lines covered (76.81%)

0.77 hits per line

Coverage Regressions

Lines Coverage ∆ File
71
67.13
-21.99% personalize.py
15
71.43
15.87% cli_personalize.py
3
94.92
0.18% gene_sets.py
Jobs
ID Job ID Ran Files Coverage
1 35369459462.1 39
76.81
GitHub Action Run
Source Files on build 35369459462