skills/bioskills/bio-proteomics-protein-inference/scripts/protein_groups.py

• apply_parsimony · function · L30-L45 — def apply_parsimony(peptide_protein_map)
• build_groups · function · L48-L66 — def build_groups(selected, protein_peptides, peptide_protein_map): # collapse proteins with identical observed-peptide evidence into one group
• picked_group_fdr · function · L69-L89 — def picked_group_fdr(groups, cutoff=FDR_CUTOFF, decoy_prefix=DECOY_PREFIX): # PICKED FDR: pair each target group with its decoy counterpart (same accessions # minus the prefix) and keep only the higher-scoring of the pair before counting.