Merge pull request #885 from biorack/fix_filter_polarity

fix: correctly pass polarity per analysis
biorack · Jul 16, 2024 · d29ee5c · d29ee5c
2 parents b636a13 + b307b7b
commit d29ee5c
Showing 1 changed file with 7 additions and 6 deletions.
diff --git a/metatlas/tools/atlas_prefilter.py b/metatlas/tools/atlas_prefilter.py
@@ -13,6 +13,7 @@
 import metatlas.plots.dill2plots as dp
 from metatlas.datastructures.analysis_identifiers import AnalysisIdentifiers
 from metatlas.datastructures.metatlas_dataset import MetatlasDataset
+from metatlas.tools.config import Analysis
 from metatlas.tools.notebook import in_papermill
 
 # Typing:
@@ -119,8 +120,8 @@ def score_ms2_data(ms2_data: pd.DataFrame, aligned_atlas_df: pd.DataFrame,
 
     ms2_data_refs_merge['ref_frags'] = ms2_data_refs_merge['spectrum_y'].apply(lambda x: len(x[0]) if x.any() else 0)
     ms2_data_refs_merge['data_frags'] = ms2_data_refs_merge['spectrum_x'].apply(lambda x: len(x[0]) if x.any() else 0)
-    ms2_data_refs_merge['reference_data_ratio'] = ms2_data_refs_merge['ref_frags']/ms2_data_refs_merge['data_frags']
-    ms2_data_refs_merge['match_reference_ratio'] = ms2_data_refs_merge['matches']/ms2_data_refs_merge['ref_frags']
+    ms2_data_refs_merge['reference_data_ratio'] = ms2_data_refs_merge['ref_frags'] / ms2_data_refs_merge['data_frags']
+    ms2_data_refs_merge['match_reference_ratio'] = ms2_data_refs_merge['matches'] / ms2_data_refs_merge['ref_frags']
 
     ms2_data_refs_merge = ms2_data_refs_merge.drop(['ref_frags', 'data_frags'], axis=1)
 
@@ -148,7 +149,7 @@ def filter_atlas_labels(ms1_data: pd.DataFrame, ms2_data_scored: pd.DataFrame, p
     return reduced_labels
 
 
-def filter_atlas(aligned_atlas, ids: AnalysisIdentifiers, analysis, data: MetatlasDataset):
+def filter_atlas(aligned_atlas, ids: AnalysisIdentifiers, analysis: Analysis, data: MetatlasDataset):
 
     aligned_atlas_df = make_atlas_df(aligned_atlas)
     sample_file_paths = get_sample_file_paths(ids)
@@ -158,14 +159,14 @@ def filter_atlas(aligned_atlas, ids: AnalysisIdentifiers, analysis, data: Metatl
     else:
         mz_tolerance = analysis.parameters.mz_tolerance_default
 
-    ms1_data, ms2_data = get_sample_data(aligned_atlas_df, sample_file_paths, mz_tolerance, data.extra_time, ids.polarity)
-    ms2_data_scored = score_ms2_data(ms2_data, aligned_atlas_df, ids.polarity,
+    ms1_data, ms2_data = get_sample_data(aligned_atlas_df, sample_file_paths, mz_tolerance, data.extra_time, analysis.parameters.polarity)
+    ms2_data_scored = score_ms2_data(ms2_data, aligned_atlas_df, analysis.parameters.polarity,
                                      analysis.parameters.msms_refs, analysis.parameters.frag_mz_tolerance)
 
     reduced_labels = filter_atlas_labels(ms1_data, ms2_data_scored, analysis.parameters.peak_height, analysis.parameters.num_points,
                                          analysis.parameters.msms_score, analysis.parameters.msms_matches, analysis.parameters.msms_frag_ratio)
 
     aligned_filtered_atlas_df = aligned_atlas_df[aligned_atlas_df['label'].isin(reduced_labels)]
-    aligned_filtered_atlas = dp.get_atlas(aligned_atlas.name, aligned_filtered_atlas_df, ids.polarity, mz_tolerance)
+    aligned_filtered_atlas = dp.get_atlas(aligned_atlas.name, aligned_filtered_atlas_df, analysis.parameters.polarity, mz_tolerance)
 
     return aligned_filtered_atlas