fix

cas9on.py

@@ -126,27 +126,29 @@ def find_crispr_targets(sequence, chr, start, strand, transcript_id, pam="NGG",
 def process_gene(gene_symbol, model_path):
     transcripts = fetch_ensembl_transcripts(gene_symbol)
     all_data = []
-    gene_sequence = ''  # Initialize an empty string for the gene sequence
 
     if transcripts:
-        cds_list = fetch_ensembl_cds(transcripts)
+        cdslist = fetch_ensembl_cds(transcripts[0].get('id'))
         for transcript in transcripts:
-            transcript_id = transcript['id']
+            transcript_id = transcript.get('id')
             chr = transcript.get('seq_region_name', 'unknown')
             start = transcript.get('start', 0)
             strand = transcript.get('strand', 'unknown')
-            # Fetch the sequence here and concatenate if multiple transcripts
-            gene_sequence += fetch_ensembl_sequence(transcript_id) or ''
-            # Fetch exon and CDS information
+            # Fetch the gene sequence for each transcript
+            gene_sequence = fetch_ensembl_sequence(transcript_id) or ''
+            # Fetch exon and CDS information is not directly used here but you may need it elsewhere
             exons = fetch_ensembl_exons(transcript_id)
+
             if gene_sequence:
-                gRNA_sites = find_crispr_targets(gene_sequence, chr, start, strand)
+                # Now correctly passing transcript_id as an argument
+                gRNA_sites = find_crispr_targets(gene_sequence, chr, start, strand, transcript_id)
                 if gRNA_sites:
                     formatted_data = format_prediction_output(gRNA_sites, model_path)
                     all_data.extend(formatted_data)
 
-    # Return the data, fetched sequence, and possibly exon/CDS data
-    return all_data, gene_sequence, exons, cds_list
+    # Return the data and potentially any other information as needed
+    return all_data, cdslist, exons
+
 
 def create_genbank_features(formatted_data):
     features = []