Merge pull request #203 from compomics/timstof_models

Timstof models
compomics · Sep 12, 2023 · a312411 · a312411
2 parents a76619a + 4d48c1c
commit a312411
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Showing 2 changed files with 27 additions and 3 deletions.
diff --git a/ms2pip/constants.py b/ms2pip/constants.py
@@ -143,5 +143,20 @@
             "model_20220104_CID_TMT_Y.xgboost": "299539179ca55d4ac82e9aed6a4e0bd134a9a41e",
         },
     },
+    "timsTOF": {
+        "id": 12,
+        "ion_types": ["B", "Y"],
+        "peaks_version": "general",
+        "features_version": "normal",
+        "xgboost_model_files": {
+            "b": "model_20230912_timsTOF_B.xgboost",
+            "y": "model_20230912_timsTOF_Y.xgboost",
+        },
+        "model_hash": {
+            "model_20230912_timsTOF_B.xgboost": "6beb557052455310d8c66311c86866dda8291f4b",
+            "model_20230912_timsTOF_Y.xgboost": "8edd87e0fba5f338d0a0881b5afbcf2f48ec5268",
+        },
+    },
 }
+
 MODELS["HCD"] = MODELS["HCD2021"]
diff --git a/ms2pip/core.py b/ms2pip/core.py
@@ -769,9 +769,18 @@ def _assemble_training_data(results: List[ProcessingResult], model: str) -> pd.D
         ]
     )
     for ion_type in ion_types:
-        training_data[f"target_{ion_type}"] = np.concatenate(
-            [r.observed_intensity[ion_type] for r in results if r.feature_vectors is not None]
-        )
+        if ion_type in ["a", "b", "b2", "c"]:
+            training_data[f"target_{ion_type}"] = np.concatenate(
+                [r.observed_intensity[ion_type] for r in results if r.feature_vectors is not None]
+            )
+        elif ion_type in ["x", "y", "y2", "z"]:
+            training_data[f"target_{ion_type}"] = np.concatenate(
+                [
+                    r.observed_intensity[ion_type][::-1]
+                    for r in results
+                    if r.feature_vectors is not None
+                ]
+            )
 
     # Reorder columns
     training_data = training_data[