feat: per-ORF P-site quantification#188
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Expand the cohort BED12 catalogue into codon-start BED6 positions (frame defined by each ORF's own ATG, not GTF `phase`), then run per-sample bedtools intersect against plastid wiggle tracks to assemble an ORF x sample count matrix. Gated on --extended_orf_analysis true + at-least-one-caller + --skip_plastid false. Matrix published under <outdir>/orf_quantification/. Uses upstream custom/bed12codonpositions (nf-core/modules#11733 pending).
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Summary
Adds a per-ORF P-site quantification path that runs additively to the existing gene-level Plastid path. Expands the cohort BED12 catalogue (#167) into codon-start BED6 positions, then runs
bedtools intersectper sample against plastid wiggle tracks and assembles an ORF x sample count matrix.Changes
QUANTIFY_ORF_PSITEchainingCUSTOM_BED12CODONPOSITIONS(cohort-level codon-start expansion) +QUANTIFY_INFRAME_PSITE_ORF(per-sample bedtools intersect + groupby) +ORF_COUNT_MATRIX(pivot to ORF x sample matrix, zero-fill for missing ORFs).quantify_inframe_psite_orf,orf_count_matrix.QUANTIFY_ORF_PSITEwhen--extended_orf_analysis true, at least one ORF caller is enabled, and plastid is not skipped.<outdir>/orf_quantification/.Codon-start counting (not span counting)
Only P-sites falling exactly at the first position of each in-frame codon are counted (positions 0, 3, 6, ... relative to each ORF's own ATG). Maximises in-frame purity at the cost of ~1/3 the raw counts vs span counting. The frame is taken from the ORF's own start codon, not from GTF
phase, so novel ORFs without GTF annotation work correctly.🚨 Upstream dependency
Uses
custom/bed12codonpositionsfrom nf-core/modules#11733 (open).modules.jsonis pinned to that PR branch. Before this PR can leave draft:master.nf-core modules install custom/bed12codonpositionssomodules.jsonshows the master SHA.Stacked PR notes
Twelfth in the stack splitting #174. Targets #187 (
feat/167-orf-catalogue).Closes #166
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