diff --git a/oktoberfest/utils/example_configs.py b/oktoberfest/utils/example_configs.py new file mode 100644 index 00000000..dd17c894 --- /dev/null +++ b/oktoberfest/utils/example_configs.py @@ -0,0 +1,56 @@ +RESCORING = { + "type": "Rescoring", + "tag": "", + "inputs": {"search_results": "msms.txt", "search_results_type": "Maxquant", "spectra": "./", "spectra_type": "raw"}, + "output": "./out", + "models": {"intensity": "Prosit_2020_intensity_HCD", "irt": "Prosit_2019_irt"}, + "prediction_server": "koina.proteomicsdb.org:443", + "ssl": True, + "thermoExe": "ThermoRawFileParser.exe", + "numThreads": 1, + "fdr_estimation_method": "mokapot", + "regressionMethod": "spline", + "allFeatures": False, + "massTolerance": 20, + "unitMassTolerance": "ppm", +} + +CECALIB = { + "type": "CollisionEnergyCalibration", + "tag": "", + "inputs": {"search_results": "msms.txt", "search_results_type": "Maxquant", "spectra": "./", "spectra_type": "raw"}, + "output": "./out", + "models": {"intensity": "Prosit_2020_intensity_HCD", "irt": "Prosit_2019_irt"}, + "prediction_server": "koina.proteomicsdb.org:443", + "ssl": True, + "thermoExe": "ThermoRawFileParser.exe", + "numThreads": 1, + "massTolerance": 20, + "unitMassTolerance": "ppm", +} + +LIBGEN = { + "type": "SpectralLibraryGeneration", + "tag": "", + "inputs": { + "search_results": "msms.txt", + "search_results_type": "Maxquant", + "library_input": "uniprot.fasta", + "library_input_type": "fasta", + }, + "output": "./out", + "models": {"intensity": "Prosit_2020_intensity_HCD", "irt": "Prosit_2019_irt"}, + "outputFormat": "spectronaut", + "prediction_server": "koina.proteomicsdb.org:443", + "ssl": True, + "fastaDigestOptions": { + "fragmentation": "HCD", + "digestion": "full", + "missedCleavages": 2, + "minLength": 7, + "maxLength": 60, + "enzyme": "trypsin", + "specialAas": "KR", + "db": "concat", + }, +}