subformula explanation

Wang-Bioinformatics-Lab · Sep 11, 2024 · 0ebad05 · 0ebad05
1 parent 0605151
commit 0ebad05
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/bin/create_library/main.py b/bin/create_library/main.py
@@ -29,7 +29,7 @@ def create_library(compound_df, feature_df,
     if df is None or df.empty:
         return None, None
 
-    if filter_library:
+    if filter_library and ms2_explanation_cutoff > 0:
         # Filter the merged dataframe
         df = filter_df(df, ion_mode, ms2_explanation_cutoff=ms2_explanation_cutoff)
 

diff --git a/bin/create_library/ms2_explanation_filter.py b/bin/create_library/ms2_explanation_filter.py
@@ -11,6 +11,11 @@ def filter_by_ms2_explanation(row, explanation_cutoff=0.60):
                                            precursor_formula=row['neutralized_formula'],
                                            adduct=row['t_adduct'],
                                            ms2_tol=0.01, ppm=False)
+
+        if subformla_list is None:  # formula elements outside common elements
+            row['ms2_explained_intensity'] = 1.0
+            return row
+
         for subformula in subformla_list:
             explained_intensity += row['MS2'][:, 1][subformula.idx] if subformula.subform_list else 0.0
         row['ms2_explained_intensity'] = explained_intensity / row['MS2'][:, 1].sum()