Mercurial > repos > sanbi-uwc > summarize_poliovirus_alignment

diff summarize_alignment.py @ 2:5c8dfc4d9d68 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
author sanbi-uwc
date Thu, 21 Jul 2022 16:43:55 +0000
parents 7e49c6b19f5e
children 7bcfc97b9284
line wrap: on
line diff
--- a/summarize_alignment.py	Tue Jul 19 11:57:59 2022 +0000
+++ b/summarize_alignment.py	Thu Jul 21 16:43:55 2022 +0000
@@ -14,6 +14,7 @@
     parser.add_argument("--datasets", nargs="+")
     args = parser.parse_args()
 
+    galaxy_metadata = {}
     summary_output = open(args.summary_output_filename, "w")
     for i, json_filename in enumerate(args.datasets):
         alignment_summary = json.load(open(json_filename))
@@ -27,6 +28,7 @@
             alignment_summary["sample_name"],
             alignment_summary["best_reference"],
             alignment_summary["mismatches"],
+            alignment_summary["perc_mismatches"],
             round(alignment_summary["quality"], 2),
             mismatch_list,
             sep="\t",