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Timstof models #203

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merged 4 commits into from
Sep 12, 2023
Merged

Timstof models #203

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e5c848e
timstof_models
ArthurDeclercq Sep 8, 2023
70a3f6d
add ms2pip timsTOF models
ArthurDeclercq Sep 12, 2023
2b4d66a
fix training data function
ArthurDeclercq Sep 12, 2023
4d48c1c
changed model filenames
ArthurDeclercq Sep 12, 2023
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15 changes: 15 additions & 0 deletions ms2pip/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"]
15 changes: 12 additions & 3 deletions ms2pip/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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[
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