--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mlstAddFields.py	Fri Jan 19 11:47:53 2024 +0000
@@ -0,0 +1,73 @@
+#!/usr/bin/env 
+
+import sys
+import csv
+
+def find_index(headers, term):
+    try:
+        return headers.index(term)
+    except ValueError:
+        return -1
+
+def main(mlst_file, db_path=None):
+    with open(mlst_file, 'r') as file:
+        reader = csv.reader(file, delimiter='\t')
+        mlstout = next(reader)
+
+    schema = mlstout[1]
+    mlstST = mlstout[2]
+
+    if db_path is None:
+        # If no database path is provided, find it using an external command
+        # This requires the 'mlst' command to be installed and available in the path
+        import subprocess
+        mlstdesc = subprocess.check_output(['mlst', '-h']).decode()
+        db_pubmlst = [line for line in mlstdesc.split('\n') if 'db/pubmlst' in line]
+        if db_pubmlst:
+            mlstloc = db_pubmlst[0].split("'")[1].replace("bin/..", "")
+        else:
+            raise Exception("Could not find MLST database location.")
+    else:
+        mlstloc = db_path
+
+    mlst_file_path = f"{mlstloc}/{schema}/{schema}.txt"
+
+    schema_dict = {}
+    with open(mlst_file_path, 'r') as file:
+        reader = csv.reader(file, delimiter='\t')
+        headers = next(reader)
+
+        clonal = find_index(headers, 'clonal_complex')
+        cc = find_index(headers, 'CC')
+        lineage = find_index(headers, 'Lineage')
+        species = find_index(headers, 'species')
+
+        for line in reader:
+            desc = []
+            if clonal > -1 and line[clonal]:
+                desc.append(f"clonal_complex={line[clonal]}")
+            if cc > -1 and line[cc]:
+                desc.append(f"CC={line[cc]}")
+            if lineage > -1 and line[lineage]:
+                desc.append(f"Lineage={line[lineage]}")
+            if species > -1 and line[species]:
+                desc.append(f"species={line[species]}")
+            schema_dict[line[0]] = ','.join(desc)
+
+    output = mlstout[:3]
+    if mlstST in schema_dict:
+        output.append(schema_dict[mlstST])
+    output.extend(mlstout[3:])
+
+    print("\t".join(output))
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Usage: python mlstAddFields.py <mlst_file> [db_path]")
+        sys.exit(1)
+
+    mlst_file = sys.argv[1]
+    db_path = sys.argv[2] if len(sys.argv) > 2 else None
+
+    main(mlst_file, db_path)
+