--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant4b.py	Fri Mar 13 12:01:17 2026 +0000
@@ -0,0 +1,54 @@
+import sys
+
+def identify_variants_with_genes(input_file_path, output_file_path, simple_name):
+    # Define the genes of interest
+    genes_of_interest = ['LMO0737', 'ORF2110', 'ORF2819']
+
+    # Open the input file and read its lines
+    with open(input_file_path, 'r') as file:
+        lines = file.readlines()
+
+    # Check if the file has more than just the header
+    if len(lines) <= 1:
+        print("Input file does not contain enough data.")
+        return
+
+    # Extract the column headers and find the indices of the genes of interest
+    headers = lines[0].strip().split('\t')
+    gene_indices = [headers.index(gene) for gene in genes_of_interest]
+    serotype_index = headers.index('SEROTYPE')
+
+    # Modify the header to include the new first column
+    modified_header = f"FileName\t{lines[0]}"
+    
+    # Initialize a list to hold the modified lines, starting with the modified header
+    modified_lines = [modified_header]
+
+    # Process each data line in the input file
+    for line in lines[1:]:
+        data = line.strip().split('\t')
+        # Check if the genes of interest are all present (marked as "FULL")
+        if all(data[index] == 'FULL' for index in gene_indices):
+            # Modify the SEROTYPE column to "4b variant"
+            data[serotype_index] = "4b variant"
+        # Prepend the simple name to the line
+        modified_line = f"{simple_name}\t" + '\t'.join(data) + '\n'
+        # Add the modified line to the list
+        modified_lines.append(modified_line)
+
+    # Write the modified lines to the output file
+    with open(output_file_path, 'w') as file:
+        file.writelines(modified_lines)
+
+    print(f'Results written to {output_file_path}')
+
+if __name__ == "__main__":
+    if len(sys.argv) != 4:
+        print("Usage: python script.py <input_file_path> <output_file_path> <simple_name>")
+        sys.exit(1)
+
+    input_file_path = sys.argv[1]
+    output_file_path = sys.argv[2]
+    simple_name = sys.argv[3]
+    identify_variants_with_genes(input_file_path, output_file_path, simple_name)
+