Revising trycycler and select assembly implementations

bin/compare_busco.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+
+import argparse
+import json
+from typing import Tuple
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "json_files",
+        metavar="FILE",
+        type=str,
+        nargs="+",
+        help="Paths to one or more BUSCO JSON files"
+    )
+    return parser.parse_args()
+
+def get_complete_buscos(json_file) -> Tuple[str, float]:
+    """
+    Get the assembler name and complete BUSCO % from a json
+    """
+    with open(json_file, 'r') as f:
+        j = json.load(f)
+        assembler = j['parameters']['out']
+        # get assembler only from e.g. barcode01_consensus_busco
+        assembler = assembler.split('_')[1]
+        assert assembler in ['flye', 'unicycler', 'consensus']
+        complete_busco = j['results']['Complete percentage']
+        return assembler, complete_busco
+
+if __name__ == "__main__":
+    args = parse_args()
+    results = [get_complete_buscos(file) for file in args.json_files]
+    highest_busco = max(results, key=lambda x: x[1])
+    print(highest_busco[0], end="") # don't print newline