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Introduction
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This codebase is being developed at Mass Dynamics https://www.massdynamics.com/ to facilitate work on the [Protein Inference Problem](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S16-S4). 

It has been developed using  the output of [crux comet/percolator](https://crux.ms/commands/percolator.html) (eg: percolator.target.psms.txt), but requires only that psm tables contain q-value and score columns, although more information about psms could theoretically be integrated into scoring methods. 

This codebase could be used for the following purposes:

    * to develop or benchmark protein inference algorithms using shared data processing and  parallelization infrastructure
    * to visualize the peptide-protein networks that are being reasoned about by a protein inference algorithm
    * to opensource an algorithm that is implimented inside this package

The REPRISAL algorithm, currently unpublished, was the first novel algorithm implemented inside the protein_inference framework and is contained in the distinct subpackage "reprisal". 

REPRISAL stands for "REcursive PRotein Inference Scoring ALgorithm" and works by iteratively scoring proteins by their associated peptides and grouping all associated and unallocated peptides with the highest scoring protein at each iteration. FDR's are then calculated as per the score distributions for proteins in the target and decoy tables.