From be9036f47ff717ea44633329e686b89b793e6037 Mon Sep 17 00:00:00 2001
From: Mario Picciani <mario.picciani@tum.de>
Date: Fri, 6 Oct 2023 15:46:33 +0200
Subject: [PATCH] added example configs

---
 oktoberfest/utils/example_configs.py | 56 ++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 oktoberfest/utils/example_configs.py

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",
+    },
+}