paper results comes from this version

wilhelm-lab · Oct 15, 2024 · 414bb2a · 414bb2a
1 parent 434f41e
commit 414bb2a
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 16 deletions.
diff --git a/spectrum_fundamentals/metrics/percolator.py b/spectrum_fundamentals/metrics/percolator.py
@@ -64,9 +64,9 @@ def __init__(
         self.all_features_flag = all_features_flag
         self.regression_method = regression_method
         self.fdr_cutoff = fdr_cutoff
-        self.xl = "CROSSLINKER_TYPE" in self.metadata.columns
-
-        super().__init__(pred_intensities, true_intensities, mz)
+
+        super().__init__(pred_intensities, true_intensities, mz, xl="CROSSLINKER_TYPE" in self.metadata.columns)
+
 
     @staticmethod
     def sample_balanced_over_bins(retention_time_df: pd.DataFrame, sample_size: int = 5000) -> pd.Index:
@@ -278,12 +278,10 @@ def add_percolator_metadata_columns(self):
         """Add metadata columns needed by percolator, e.g. to identify a PSM."""
         if self.xl:
             spec_id_cols = ["RAW_FILE", "SCAN_NUMBER", "MODIFIED_SEQUENCE_A", "MODIFIED_SEQUENCE_B", "PRECURSOR_CHARGE"]
-            self.metrics_val["Peptide"] = (
-                self.metadata["MODIFIED_SEQUENCE_A"] + "_" + self.metadata["MODIFIED_SEQUENCE_B"]
-            ).apply(lambda x: "_." + x + "._")
-            self.metrics_val["Proteins"] = (
-                self.metadata["MODIFIED_SEQUENCE_A"] + "_" + self.metadata["MODIFIED_SEQUENCE_B"]
-            )
+            modified_sequence_a = self.metadata["MODIFIED_SEQUENCE_A"].astype(str)
+            modified_sequence_b = self.metadata["MODIFIED_SEQUENCE_B"].astype(str)
+            self.metrics_val["Peptide"] = (modified_sequence_a + "_" + modified_sequence_b).apply(lambda x: "_." + x + "._")
+            self.metrics_val["Proteins"] = (modified_sequence_a + "_" + modified_sequence_b)
             self.metrics_val["Label"] = self.target_decoy_labels
         else:
             spec_id_cols = ["RAW_FILE", "SCAN_NUMBER", "MODIFIED_SEQUENCE", "PRECURSOR_CHARGE"]
@@ -466,10 +464,10 @@ def calc(self):
             # self.metrics_val['spectral_angle_delta_score'] = Percolator.get_delta_score(self.metrics_val[['ScanNr',
             # 'spectral_angle']], 'spectral_angle')
             pass
-        else:
-            self.metrics_val["andromeda_delta_score"] = Percolator.get_delta_score(
-                self.metrics_val[["ScanNr", "andromeda"]], "andromeda"
-            )
+        #else:
+           # self.metrics_val["andromeda_delta_score"] = Percolator.get_delta_score(
+               # self.metrics_val[["ScanNr", "andromeda"]], "andromeda"
+           # )
 
         self._reorder_columns_for_percolator()
 

diff --git a/spectrum_fundamentals/metrics/similarity.py b/spectrum_fundamentals/metrics/similarity.py
@@ -481,9 +481,7 @@ def _calc_additional_metrics(
             true_intensities, pred_intensities, "max"
         )
         self.metrics_val[f"mse{key_suffix}"] = SimilarityMetrics.abs_diff(true_intensities, pred_intensities, "mse")
-        self.metrics_val[f"modified_cosine{key_suffix}"] = SimilarityMetrics.modified_cosine(
-            true_intensities, pred_intensities, self.mz, self.mz
-        )
+
 
         col_names_spectral_angle = [
             f"spectral_angle_{amount}_charge{key_suffix}" for amount in ["single", "double", "triple"]
@@ -539,3 +537,7 @@ def _calc_additional_metrics(
                 self.metrics_val[col_name_spearman_corr] = SimilarityMetrics.correlation(
                     true_intensities, pred_intensities, i + 1, "spearman"
                 )
+
+            self.metrics_val[f"modified_cosine{key_suffix}"] = SimilarityMetrics.modified_cosine(
+            true_intensities, pred_intensities, self.mz, self.mz
+                )