Add quick fixes and todos addressing comments on #378

alphastats/dataset/dataset.py

@@ -151,12 +151,31 @@ def _check_loader(loader):
             )
 
     def _create_id_dicts(self, sep: str = ";") -> Tuple[dict, dict, dict]:
-        """Create mapprings from gene, protein to feature and from feature to repr."""
+        """
+        Create mappings from gene and protein to feature, and from feature to representation.
+        Features are the entities measured in each sample, usually protein groups represented by semicolon separated protein ids.
+        This is to maintain the many-to-many relationships between the three entities feature, protein and gene.
+
+        This method processes the raw input data to generate three dictionaries:
+        1. gene_to_features_map: Maps each gene to a list of features.
+        2. protein_to_features_map: Maps each protein to a list of features.
+        3. feature_to_repr_map: Maps each feature to its representation string.
+
+        Args:
+            sep (str): The separator used to split gene and protein identifiers. Default is ";".
+
+        Returns:
+            Tuple[dict, dict, dict]: A tuple containing three dictionaries:
+            - gene_to_features_map (dict): A dictionary mapping genes to features.
+            - protein_to_features_map (dict): A dictionary mapping proteins to features.
+            - feature_to_repr_map (dict): A dictionary mapping features to their representation strings.
+        """
 
         features = self.mat.columns.to_list()
-        gene_to_features_map = defaultdict(lambda: [])
-        protein_to_features_map = defaultdict(lambda: [])
-        feature_to_repr_map = defaultdict(lambda x: x)
+        gene_to_features_map = defaultdict(list)
+        protein_to_features_map = defaultdict(list)
+        feature_to_repr_map = {}
+        # TODO: Make sure both iterators are with zip after merging branches.
 
         for proteins, feature in self.rawinput[[Cols.INDEX, Cols.INDEX]].itertuples(
             index=False
@@ -469,7 +488,8 @@ def _get_features_for_gene_name(
         self,
         gene_name: str,
     ) -> list:
-        """Get protein groups from gene id. If gene id is not present, return gene id, as we might already have a gene id.
+        # TODO: This should raise an error and not return the gene name if it is not actually in the data.
+        """Get feature from gene name. If gene name is not present, return gene name, as we might already have a gene id.
         'HEL114' -> ['P18206;A0A024QZN4;V9HWK2;B3KXA2;Q5JQ13;B4DKC9;B4DTM7;A0A096LPE1']
 
         Args:

alphastats/loader/maxquant_loader.py

@@ -46,11 +46,13 @@ def __init__(
         self._set_filter_columns_to_true_false()
         self._read_all_column_names_as_string()
 
+        # TODO externalize to a method
         intensity_columns = [
             col
             for col in self.rawinput.columns
             if intensity_column.replace("[sample]", "") in col
         ]
+        # TODO: explain why we do this
         if len(self.rawinput.dropna(subset=intensity_columns, how="all")) != len(
             self.rawinput
         ):

alphastats/plots/intensity_plot.py

@@ -59,6 +59,7 @@ def __init__(
         self.method = method
         self.add_significance = add_significance
         self.log_scale = log_scale
+        # TODO: rename y_axis to make clear this is not a name from the original data
         self.y_axis = self.intensity_column.replace("[sample]", "").strip()
         if self.preprocessing_info[PreprocessingStateKeys.LOG2_TRANSFORMED]:
             self.y_axis = "log2(" + self.y_axis + ")"
@@ -139,7 +140,6 @@ def _add_significance(plot):
         return plot
 
     def _prepare_data(self):
-        # TODO use difflib to find similar ProteinId if ProteinGroup is not present
         df = (
             self.mat[self.protein_id].melt(
                 ignore_index=False,

tests/test_dataset.py

@@ -1061,6 +1061,7 @@ def test_preprocess_replace_zero(self):
         )
 
     def test_create_id_mapping(self):
+        # TODO: Test the actual dicts.
         """Test id maps"""
         self.assertEqual(len(self.obj._gene_to_features_map), 21)
         self.assertEqual(len(self.obj._gene_to_features_map["G14"]), 2)