diff assess_alignment.py @ 5:0e556a3f85d6 draft

planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty

--- a/assess_alignment.py	Fri Jul 22 09:55:46 2022 +0000
+++ b/assess_alignment.py	Wed Sep 14 09:21:44 2022 +0000
@@ -145,11 +145,13 @@
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument("--output_filename", help="Path to output file")
+    parser.add_argument("--consensus_output_filename", help="Path to output file for best consensus")
     parser.add_argument("--sample_name", help="Name of sample being analysed")
     parser.add_argument(
         "--dataset_names", type=comma_split, help="Comma separated names for datasets"
     )
     parser.add_argument("--datasets", nargs="+")
+    parser.add_argument("--consensi", nargs="+")
     args = parser.parse_args()
 
     offsets = {
@@ -182,6 +184,7 @@
             best_match_mismatch_list = mismatch_list
             best_match_quality = quality
             best_match_reference = dataset_name
+            best_consensus = args.consensi[file_index]
             percent_mismatches = round(min_mismatches / lengths[best_match_reference] * 100, 2)
 
     info = {
@@ -190,6 +193,8 @@
         "mismatches": min_mismatches,
         "mismatch_list": best_match_mismatch_list,
         "quality": best_match_quality,
-        "perc_mismatches": percent_mismatches
+        "perc_mismatches": percent_mismatches,
     }
     json.dump(info, open(args.output_filename, "w"))
+
+    open(args.consensus_output_filename, "w").write(best_consensus)