risk-network 0.0.9b33__tar.gz → 0.0.9b34__tar.gz

{risk_network-0.0.9b33 → risk_network-0.0.9b34}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b33
+Version: 0.0.9b34
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.9b33 → risk_network-0.0.9b34}/risk/__init__.py

@@ -7,4 +7,4 @@ RISK: Regional Inference of Significant Kinships
 
 from risk.risk import RISK
 
-__version__ = "0.0.9-beta.33"
+__version__ = "0.0.9-beta.34"

{risk_network-0.0.9b33 → risk_network-0.0.9b34}/risk/neighborhoods/api.py

@@ -280,7 +280,7 @@ class NeighborhoodsAPI:
         null_distribution: str = "network",
         random_seed: int = 888,
     ) -> Dict[str, Any]:
-        """Load significant neighborhoods for the network using the Z-score test.
+        """Load significant neighborhoods for the network using the z-score test.
 
         Args:
             network (nx.Graph): The network graph.
@@ -299,8 +299,8 @@ class NeighborhoodsAPI:
         Returns:
             Dict[str, Any]: Computed significance of neighborhoods.
         """
-        log_header("Running Z-score test")
-        # Compute neighborhood significance using the Z-score test
+        log_header("Running z-score test")
+        # Compute neighborhood significance using the z-score test
         return self._load_neighborhoods_by_statistical_test(
             network=network,
             annotations=annotations,

{risk_network-0.0.9b33 → risk_network-0.0.9b34}/risk/network/io.py

@@ -262,8 +262,25 @@ class NetworkIO:
             attribute_table.columns = attribute_table.iloc[0]
             # Skip first four rows, select source and target columns, and reset index
             attribute_table = attribute_table.iloc[4:, :]
-            attribute_table = attribute_table[[source_label, target_label]]
+            try:
+                # Attempt to filter the attribute_table with the given labels
+                attribute_table = attribute_table[[source_label, target_label]]
+            except KeyError as e:
+                # Find which key(s) caused the issue
+                missing_keys = [
+                    key
+                    for key in [source_label, target_label]
+                    if key not in attribute_table.columns
+                ]
+                # Raise the KeyError with details about the issue and available options
+                available_columns = ", ".join(attribute_table.columns)
+                raise KeyError(
+                    f"The column(s) '{', '.join(missing_keys)}' do not exist in the table. "
+                    f"Available columns are: {available_columns}."
+                ) from e
+
             attribute_table = attribute_table.dropna().reset_index(drop=True)
+
             # Create a graph
             G = nx.Graph()
             # Add edges and nodes
@@ -271,7 +288,6 @@ class NetworkIO:
                 source = row[source_label]
                 target = row[target_label]
                 G.add_edge(source, target)
-
                 if source not in G:
                     G.add_node(source)  # Optionally add x, y coordinates here if available
                 if target not in G:

{risk_network-0.0.9b33 → risk_network-0.0.9b34}/risk/stats/stat_tests.py

@@ -215,7 +215,7 @@ def compute_zscore_test(
     null_distribution: str = "network",
 ) -> Dict[str, Any]:
     """
-    Compute Z-score test for enrichment and depletion in neighborhoods with selectable null distribution.
+    Compute z-score test for enrichment and depletion in neighborhoods with selectable null distribution.
 
     Args:
         neighborhoods (csr_matrix): Sparse binary matrix representing neighborhoods.
@@ -257,10 +257,10 @@ def compute_zscore_test(
         * (1 - neighborhood_sums / background_population)
     )
     std_dev[std_dev == 0] = np.nan  # Avoid division by zero
-    # Compute Z-scores
+    # Compute z-scores
     z_scores = (observed - expected) / std_dev
 
-    # Convert Z-scores to depletion and enrichment p-values
+    # Convert z-scores to depletion and enrichment p-values
     enrichment_pvals = norm.sf(z_scores)  # Upper tail
     depletion_pvals = norm.cdf(z_scores)  # Lower tail
 

{risk_network-0.0.9b33 → risk_network-0.0.9b34}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: risk-network
-Version: 0.0.9b33
+Version: 0.0.9b34
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>