oktoberfest.re.rescore_with_mokapot

oktoberfest.re.rescore_with_mokapot(input_file, output_folder=None, test_fdr=0.01, xl=False)

Rescore using mokapot.

The function takes an input file location, as well as an output folder location for mokapot outputs and executes mokapot with additional optional parameters.

Parameters:

  • input_file (str | Path) – Path to percolator tab file

  • output_folder (str | Path | None) – An optional output folder for all percolator files, default is the parent directory of the input_file

  • test_fdr (float) – the fdr cutoff for the test set

  • xl (bool) – crosslinked or linear peptide (currently unused)

Raises:

FileNotFoundError – if the input file does not exist