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Change input of Peptonizer to (peptide, confidence_score) maps #5
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pverscha
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Historically, the peptonizer pipeline required a PSMS-file as input (generated by tools such as Percolator or ms2rescore). However, the only information that the peptonizer really needs are peptide sequences and their associated confidence scores (produced by a search engine). We've decided that the responsibility of parsing PSMS-files is not part of the Peptonizer and that it's input will start from peptide -> confidence score maps.
This PR removes the specific parsing options for pout-files and ms2rescore files from the Peptonizer package and updates the package itself to start from a dictionary that contains the peptide -> confidence score map instead.
The snakemake workflow has remained unchanged, and can still start with PSMS-files as input. The parsing of these files has been moved to the workflow itself, since we don't want to contaminate the Peptonizer package itself with this parsing code.