pirl-unc / tsarina / 35375639021
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Files 39
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coverage: 77.117% (+0.2%) from 76.961%
35375639021

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Roll up identical-protein CTA paralogs by default; sniff --output's extension (#163)

Proteoform roll-up (new, default on): CTAs that translate to a
byte-identical protein are now reported as one group -- NY-ESO-1 as
CTAG1A/CTAG1B, plus XAGE1A/XAGE1B, SSX2/SSX2B, SSX4/SSX4B,
MAGEA2/MAGEA2B and the CT45A/CT47A/GAGE12 families. The grouping reads
oncoref.proteoforms' canonical CTA registry, the same one
tsarina.spanning already uses for the panel workflow, rather than a
second definition that could drift from it.

personalize was the only workflow not doing this, and it cut both
ways: naming one member reported it as if its peptides were unique to
that gene, and naming both reported the same peptide twice as two
findings. Now a group keeps the highest TPM any member reported
(identical proteins, so an RNA quantifier splits reads between the
loci more or less arbitrarily; summing would inflate one real signal)
and the union of their gene IDs. --no-proteoform-rollup opts out.
Viral, mutant, and ungrouped CTA rows are untouched, since a
same-peptide duplicate there can be a genuinely distinct source.

--output extension sniffing: `-o out.csv` writes CSV, `-o out.txt`
writes the table, `-o out.tsv`/`.tab` writes tab-separated (new tsv
format), anything else still defaults to CSV, and an explicit --format
always wins. Previously any --output path got CSV regardless of what
the filename said.

Bumps 1.29.0 -> 1.30.0.

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

3188 of 4134 relevant lines covered (77.12%)

0.77 hits per line

Coverage Regressions

Lines Coverage ∆ File
68
74.22
2.62% personalize.py
19
68.89
1.8% cli_personalize.py
Jobs
ID Job ID Ran Files Coverage
1 35375639021.1 39
77.12
GitHub Action Run
Source Files on build 35375639021