taxonomy split fix

ngtax_to_biom.py

@@ -140,7 +140,7 @@ def process_rdf_files(rdf_file):
 def biom_preformatter():
     # Format tax matrix a bit so further parsing as added prefixes
     tax_df = process_tax()
-    
+        
     # Load and transform the ASV file into a matrix
     lines = []
     for line in open("asv.tsv"):
@@ -218,9 +218,12 @@ def tsv_to_biom():
     
     # Create Python object from JSON string data
     obj = json.loads(json_data)
-    
+    # Fix taxonomy split issue
+    for index, row in enumerate(obj["rows"]):
+        row['metadata']['taxonomy'] = row['metadata']['taxonomy'].split("; ")
     # Pretty Print JSON
     json_formatted_str = json.dumps(obj, indent=4, sort_keys=True)
+    
     biom_file = job.split("/")[-1].replace(".job", ".biom")
     print("Writing biom file to", biom_file)
     print(json_formatted_str, file=open(biom_file, "w"))