Update app.py

app.py

@@ -5,7 +5,7 @@ import numpy as np
 from itertools import product
 import torch.nn as nn
 import matplotlib.pyplot as plt
-import matplotlib.colors as mcolors
+import matplotlib.colors as mcolors LinearSegmentedColormap
 import io 
 from io import BytesIO # Import io then BytesIO 
 from PIL import Image, ImageDraw, ImageFont
@@ -16,6 +16,9 @@ import pandas as pd
 import tempfile
 import os
 from typing import List, Dict, Tuple, Optional, Any
+import io
+from io import BytesIO
+import seaborn as sns
 
 ###############################################################################
 # 1. MODEL DEFINITION
@@ -567,18 +570,6 @@ def analyze_sequence_comparison(file1, file2, fasta1="", fasta2=""):
 # 11. GENE FEATURE ANALYSIS
 ###############################################################################
 
-import io
-from io import BytesIO
-from PIL import Image, ImageDraw, ImageFont
-import numpy as np
-import pandas as pd
-import tempfile
-import os
-from typing import List, Dict, Tuple, Optional, Any
-import matplotlib.pyplot as plt
-from matplotlib.colors import LinearSegmentedColormap
-import seaborn as sns
-
 def parse_gene_features(text: str) -> List[Dict[str, Any]]:
     """Parse gene features from text file in FASTA-like format"""
     genes = []
@@ -653,6 +644,19 @@ def compute_gene_statistics(gene_shap: np.ndarray) -> Dict[str, float]:
 
 def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_length: int) -> Image.Image:
     """Create a simple genome diagram using PIL"""
+    # Validate inputs
+    if not gene_results or genome_length <= 0:
+        img = Image.new('RGB', (800, 100), color='white')
+        draw = ImageDraw.Draw(img)
+        draw.text((10, 40), "Error: Invalid input data", fill='black')
+        return img
+        
+    # Ensure all gene coordinates are valid integers
+    for gene in gene_results:
+        gene['start'] = max(0, int(gene['start']))
+        gene['end'] = min(genome_length, int(gene['end']))
+        if gene['start'] >= gene['end']:
+            print(f"Warning: Invalid coordinates for gene {gene['gene_name']}: {gene['start']}-{gene['end']}")
     # Image dimensions
     width = 1500
     height = 600
@@ -684,7 +688,7 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
     
     # Draw scale markers
     for i in range(0, genome_length + 1, genome_length // 10):
-        x = margin + i * scale
+        x = int(margin + i * scale)
         draw.line([(x, line_y - 5), (x, line_y + 5)], fill='black', width=1)
         draw.text((x - 20, line_y + 10), f"{i:,}", fill='black', font=font)
     
@@ -693,9 +697,9 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
     
     # Draw genes
     for gene in sorted_genes:
-        # Calculate position
-        start_x = margin + gene['start'] * scale
-        end_x = margin + gene['end'] * scale
+        # Calculate position and ensure integers
+        start_x = int(margin + gene['start'] * scale)
+        end_x = int(margin + gene['end'] * scale)
         
         # Calculate color based on SHAP value
         if gene['avg_shap'] > 0:
@@ -705,10 +709,10 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
             intensity = min(255, int(abs(gene['avg_shap'] * 500)))
             color = (255 - intensity, 255 - intensity, 255)  # Blue
         
-        # Draw gene box
+        # Draw gene box with integer coordinates
         draw.rectangle([
-            (start_x, line_y - track_height // 2),
-            (end_x, line_y + track_height // 2)
+            (start_x, int(line_y - track_height // 2)),
+            (end_x, int(line_y + track_height // 2))
         ], fill=color, outline='black')
         
         # Draw gene name
@@ -726,8 +730,8 @@ def create_simple_genome_diagram(gene_results: List[Dict[str, Any]], genome_leng
         gene_width = end_x - start_x
         if gene_width > label_width:
             # Horizontal label
-            text_x = start_x + (gene_width - label_width) // 2
-            draw.text((text_x, text_y), label, fill='black', font=font)
+            text_x = int(start_x + (gene_width - label_width) // 2)
+            draw.text((text_x, int(text_y)), label, fill='black', font=font)
         elif gene_width > 20:
             # Create rotated text image
             txt_img = Image.new('RGBA', (label_width, 20), (255, 255, 255, 0))