fix

cas9on.py

@@ -208,9 +208,14 @@ def create_bigwig(df, bigwig_path):
     if not all(column in df.columns for column in ["Chr", "Start Pos", "End Pos", "Prediction"]):
         raise ValueError("DataFrame must contain 'Chr', 'Start Pos', 'End Pos', and 'Prediction' columns.")
 
-    # Convert positions to integers and prepare the BigWig header
+    # Convert positions to integers
     df['Start Pos'] = df['Start Pos'].astype(int)
     df['End Pos'] = df['End Pos'].astype(int)
+
+    # Sort the DataFrame by chromosome and start position
+    df = df.sort_values(by=['Chr', 'Start Pos'])
+
+    # Prepare the BigWig header
     chr_sizes = df.groupby('Chr')['End Pos'].max().to_dict()
     header = [(chr, int(size)) for chr, size in chr_sizes.items()]
 
@@ -219,8 +224,12 @@ def create_bigwig(df, bigwig_path):
     bw.addHeader(header)
 
     # Add entries to the BigWig file
-    for _, row in df.iterrows():
-        bw.addEntries([row['Chr']], [row['Start Pos']], ends=[row['End Pos']], values=[float(row['Prediction'])])
+    for chr, group in df.groupby('Chr'):
+        starts = group['Start Pos'].tolist()
+        ends = group['End Pos'].tolist()
+        values = group['Prediction'].astype(float).tolist()
+        bw.addEntries(chr, starts, ends=ends, values=values)
 
     # Close the BigWig file
     bw.close()
+