bugfix: MAF robustness — createinput comment lines + compute_fitness input guards - #252
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bugfix: MAF robustness — createinput comment lines + compute_fitness input guards#252johnoooh wants to merge 2 commits into
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create_phylowgs_inputs.py uses csv.DictReader on the raw MAF, so a leading "#" header/comment line gets treated as the column header row and breaks column-name based parsing (KeyError downstream). Strip any "^#" lines into filtered_head.maf before passing it as the --vcf-type input. Adds an nf-test case (with a small local MAF fixture carrying a leading "#" comment line) that reproduces and verifies the fix.
Neoantigen scoring computed logC/logA/quality unconditionally, which divided by zero when Kd or KdWT was 0 and raised a KeyError from EpitopeDistance when a peptide contained a non-standard residue (e.g. "*", "X" from stop-gained/ambiguous calls). Extract the scoring step into score_neoantigen() and zero out logC/logA/quality whenever Kd/KdWT is 0 or either sequence contains residues outside the standard 20 amino acids, instead of crashing or dividing by zero. Adds pytest coverage for the non-standard-residue guard, the Kd/KdWT guard, and a clean-input case confirming normal scoring is unaffected.
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Two independent robustness fixes surfaced by a large production run.
Fixes
phylowgs/createinput: strip leading#comment/header lines from the MAF (grep -v '^#') beforecreate_phylowgs_inputs.py, which otherwise mis-parses a commented header.neoantigenediting/computefitness: guard the scoring loop against div-by-zero (Kd/KdWT==0) and non-standard amino-acid residues (outsideACDEFGHIKLMNPQRSTVWY, e.g.*/X) which crashEpitopeDistance; zero the score components instead of raising. Guard extracted into a testablescore_neoantigen()helper.Tests
#regression case) and computefitness 2/2,--profile docker.