fix

cas9on.py

@@ -68,6 +68,15 @@ def fetch_ensembl_sequence(transcript_id):
         print(f"Error fetching sequence data from Ensembl: {response.text}")
         return None
 
+def fetch_ensembl_cds(transcript_id):
+    url = f"https://rest.ensembl.org/overlap/id/{transcript_id}?feature=cds;content-type=application/json"
+    response = requests.get(url)
+    if response.status_code == 200:
+        cds_data = response.json()
+        return cds_data
+    else:
+        print(f"Error fetching CDS data from Ensembl: {response.text}")
+        return []
 def find_crispr_targets(sequence, chr, start, strand, transcript_id, pam="NGG", target_length=20):
     targets = []
     len_sequence = len(sequence)
@@ -115,7 +124,7 @@ def process_gene(gene_symbol, model_path):
     if transcripts:
         for i in range(len(transcripts)):
             Exons = transcripts[i]['Exon']
-            cds = transcripts[i]['cds']
+            cds_list = fetch_ensembl_cds(transcript_id)
             transcript_id = transcripts[i]['display_name']
             for j in range(len(Exons)):
                 exon_id = Exons[j]['id']
@@ -137,7 +146,7 @@ def process_gene(gene_symbol, model_path):
         print("Failed to retrieve transcripts.")
 
     # Note: Returning last exon's sequence, might need adjustment based on use-case
-    return results, gene_sequence, Exons, cds
+    return results, gene_sequence, Exons, cds_list
 
 def create_genbank_features(formatted_data):
     features = []