Update app.py

app.py

@@ -3,7 +3,7 @@ import streamlit as st
 import pandas as pd
 from Bio import SeqIO
 from Bio.SeqUtils.ProtParam import ProteinAnalysis
-from Bio.Graphics import GenomeDiagram
+from Bio.Graphics.GenomeDiagram import Diagram, Track, FeatureSet
 from reportlab.lib import colors
 from reportlab.lib.units import cm
 from io import StringIO
@@ -76,23 +76,58 @@ def add_protein_features(cds_info):
             cds['Isoelectric Point'] = 'N/A'
     return cds_info
 
-# Function to generate genome diagram
+# Updated Function to generate genome diagram
 def create_genome_diagram(genbank_content, output_file_path, colors_dict, diagram_type="linear", diagram_size=(30, 10)):
     record = SeqIO.read(StringIO(genbank_content), "genbank")
-    gd_diagram = GenomeDiagram.Diagram(record.id)
-    gd_track_for_features = gd_diagram.new_track(1, name="Annotated Features")
-    gd_feature_set = gd_track_for_features.new_set()
-
+    gd_diagram = Diagram(record.id)
+    
+    # Create separate tracks for different feature types
+    max_tracks = len(colors_dict)
+    track_indices = {feature_type: idx+1 for idx, feature_type in enumerate(colors_dict.keys())}
+    feature_tracks = {}
+    for feature_type, idx in track_indices.items():
+        feature_tracks[feature_type] = gd_diagram.new_track(
+            idx, name=feature_type, scale=False, greytrack=False, height=0.5
+        )
+        feature_tracks[feature_type].new_set()
+    
     for feature in record.features:
         feature_type = feature.type
         if feature_type in colors_dict:
             color = colors.HexColor(colors_dict[feature_type])
-            gd_feature_set.add_feature(feature, color=color, label=True, label_size=10, label_angle=0)
-
+            # Adjust label parameters to minimize overlap
+            feature_set = feature_tracks[feature_type].sets[0]
+            feature_set.add_feature(
+                feature,
+                color=color,
+                label=True,
+                label_size=6,  # Decreased label size
+                label_angle=0,
+                label_position="start",  # Position label at the start of the feature
+                label_strand=1 if feature.strand == 1 else -1,  # Position labels according to strand
+                sigil="ARROW",  # Use arrows to represent features
+                arrowshaft_height=1.0,
+                arrowhead_length=1.0,
+            )
+    
     if diagram_type.lower() == "circular":
-        gd_diagram.draw(format="circular", circular=True, pagesize=(diagram_size[0]*cm, diagram_size[1]*cm), start=0, end=len(record), circle_core=0.7)
+        gd_diagram.draw(
+            format="circular",
+            circular=True,
+            pagesize=(diagram_size[0]*cm, diagram_size[1]*cm),
+            start=0,
+            end=len(record),
+            circle_core=0.7
+        )
     else:
-        gd_diagram.draw(format="linear", pagesize=(diagram_size[0]*cm, diagram_size[1]*cm), fragments=1, start=0, end=len(record))
+        gd_diagram.draw(
+            format="linear",
+            pagesize=(diagram_size[0]*cm, diagram_size[1]*cm),
+            fragments=1,
+            start=0,
+            end=len(record),
+            tracklines=False  # Remove track lines to reduce clutter
+        )
     gd_diagram.write(output_file_path, "SVG")
 
 # Function to search for a motif or pattern within the DNA sequence