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Fix preprocessing export and filtering logic #2

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Merged
baudrly merged 1 commit into from
Oct 19, 2025
Merged

Fix preprocessing export and filtering logic #2

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18 changes: 12 additions & 6 deletions src/clop/data_utils/preprocessing.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
import os

import numpy as np
import pandas as pd
from matplotlib import pyplot as plt


Expand Down Expand Up @@ -72,13 +75,16 @@ def preprocess_inputs(path, path_save):
sequences = df[input_column]
labels = df[label_column]

labels = sequences[~sequences.str.contains("U|O")]
sequences = sequences[~sequences.str.contains("U|O")]
dna_sequences = sequences.apply(protein_to_dna)
mask = ~sequences.str.contains("U|O", na=False)
filtered_labels = labels[mask]
filtered_sequences = sequences[mask]
dna_sequences = filtered_sequences.apply(protein_to_dna)

labels.save(path_save + "labels.csv")
dna_sequences.save(path_save + "sequences.csv")
print("saved processed sequences and labels (annotations")
labels_path = os.path.join(path_save, "labels.csv")
sequences_path = os.path.join(path_save, "sequences.csv")
filtered_labels.to_csv(labels_path, index=False)
dna_sequences.to_csv(sequences_path, index=False)
print("saved processed sequences and labels (annotations)")


if __name__ == "__main__":
Expand Down