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added in percolator some lines for protein column
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“Karim committed Jan 22, 2024
1 parent 2008695 commit bcb2ada
Showing 1 changed file with 1 addition and 6 deletions.
7 changes: 1 addition & 6 deletions spectrum_fundamentals/metrics/percolator.py
Original file line number Diff line number Diff line change
Expand Up @@ -273,13 +273,8 @@ def add_percolator_metadata_columns(self):
self.metrics_val["Label"] = self.target_decoy_labels
self.metrics_val["ScanNr"] = self.metadata["SCAN_NUMBER"]
self.metrics_val["filename"] = self.metadata["RAW_FILE"]
# here you should ExpMass
self.metrics_val["ExpMass"] =
self.metrics_val["Peptide"] = self.metadata["MODIFIED_SEQUENCE"].apply(lambda x: "_." + x + "._")

self.metrics_val["Proteins"] = self.metadata[
"PROTEINS"
] # added proteins column for de-duplication purposes
self.metrics_val["Proteins"] = self.metadata["PROTEINS"] # added proteins column for de-duplication purposes

def apply_lda_and_get_indices_below_fdr(
self, initial_scoring_feature: str = "spectral_angle", fdr_cutoff: float = 0.01
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