Fix build_reaction_expression to support direct gene ID matching

Fixed issue where reaction expression values were blank when converting
from gene-level to reaction-level expression.

The problem occurred when expression data was loaded without a genome
or when model gene IDs didn't match genome feature IDs. The original
code only searched through the genome object, failing to find genes
with different ID formats (e.g., model has ACIAD#### but expression
has ACIAD_RS#####).

Changes:
- First attempt direct lookup in self.features by gene ID
- Fall back to genome search (which supports aliases) if direct lookup fails
- This allows matching when gene IDs are identical, even without a genome
- Maintains backward compatibility with genome-based alias resolution

Fixes blank reaction expression values in genome-to-model conversion.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: Christopher Henry

modelseedpy/multiomics/msexpression.py

@@ -497,25 +497,34 @@ def build_reaction_expression(self, model, default: Optional[float] = None) -> '
         # Pulling the gene values from the current expression using DataFrame
         values = {}
         for gene in model.genes:
-            feature = self.object.search_for_gene(gene.id)
-            if feature is None:
-                logger.debug(
-                    "Model gene " + gene.id + " not found in genome or expression"
-                )
-            elif feature.id not in self.features:
-                logger.debug(
-                    "Model gene " + gene.id + " in genome but not in expression"
-                )
+            # First, try to find the gene directly in expression features
+            # This handles cases where expression was loaded without a genome
+            if gene.id in self.features:
+                feature = self.features.get_by_id(gene.id)
             else:
+                # Fallback: search through the genome object (supports aliases)
+                feature = self.object.search_for_gene(gene.id)
+                if feature is None:
+                    logger.debug(
+                        "Model gene " + gene.id + " not found in genome or expression"
+                    )
+                    continue
+                if feature.id not in self.features:
+                    logger.debug(
+                        "Model gene " + gene.id + " in genome but not in expression"
+                    )
+                    continue
                 feature = self.features.get_by_id(feature.id)
-                for condition in self.conditions:
-                    if condition.id not in values:
-                        values[condition.id] = {}
-                    # Get value from DataFrame instead of feature.values dictionary
-                    if feature.id in self._data.index and condition.id in self._data.columns:
-                        value = self._data.loc[feature.id, condition.id]
-                        if not pd.isna(value):
-                            values[condition.id][gene.id] = value
+
+            # Extract expression values for this feature
+            for condition in self.conditions:
+                if condition.id not in values:
+                    values[condition.id] = {}
+                # Get value from DataFrame instead of feature.values dictionary
+                if feature.id in self._data.index and condition.id in self._data.columns:
+                    value = self._data.loc[feature.id, condition.id]
+                    if not pd.isna(value):
+                        values[condition.id][gene.id] = value
 
         # Computing the reaction level values
         for condition in rxnexpression.conditions: