added example configs

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",
+    },
+}