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add intensities & sqrt intensities and fix output data
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@maim02
maim02 committed Jan 2, 2024
1 parent f0dfb20 commit 12487b6
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Showing 3 changed files with 18 additions and 5 deletions.
13 changes: 13 additions & 0 deletions oktoberfest/predict/predict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import re
from typing import Dict, Tuple

import math
import numpy as np
import pandas as pd
from spectrum_fundamentals.metrics.similarity import SimilarityMetrics
Expand Down Expand Up @@ -34,6 +35,7 @@ def predict(data: pd.DataFrame, *args, **kwargs) -> Dict[str, np.ndarray]:
"PRECURSOR_CHARGE": "precursor_charges",
"COLLISION_ENERGY": "collision_energies",
"FRAGMENTATION": "fragmentation_types",
"SUM_INTENSITIES": "sum_intensities",
},
inplace=True,
)
Expand All @@ -46,10 +48,21 @@ def predict(data: pd.DataFrame, *args, **kwargs) -> Dict[str, np.ndarray]:
"precursor_charges": "PRECURSOR_CHARGE",
"collision_energies": "COLLISION_ENERGY",
"fragmentation_types": "FRAGMENTATION",
"sum_intensities": "SUM_INTENSITIES",
},
inplace=True,
)

# todo perform square rooting of intensities here
if "model_name" in kwargs:
if "sqrt" in kwargs["model_name"]:
intensities = []
for mod_seq in results:
sqrt_intensity = []
for intensity in mod_seq:
sqrt_intensity.append(math.sqrt(intensity))
intensities.append(sqrt_intensity)
results["intensities"] = intensities
return results


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2 changes: 1 addition & 1 deletion oktoberfest/preprocessing/preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -384,7 +384,7 @@ def annotate_spectral_library(psms: Spectra, mass_tol: Optional[float] = None, u
psms.spectra_data.drop(columns=["INTENSITIES", "MZ"], inplace=True) # TODO check if this is needed
psms.add_matrix(df_annotated_spectra["INTENSITIES"], FragmentType.RAW)
psms.add_matrix(df_annotated_spectra["MZ"], FragmentType.MZ)
psms.add_column(df_annotated_spectra["SUM_INTENSITIES"], "SUM_INTENSITIES")
psms.add_column(df_annotated_spectra["LOG_SUM_INTENSITIES"].to_numpy(), "LOG_SUM_INTENSITIES")
psms.add_column(df_annotated_spectra["CALCULATED_MASS"].to_numpy(), "CALCULATED_MASS")


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8 changes: 4 additions & 4 deletions tests/unit_tests/data/predictions/library_output.csv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
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