Mercurial > repos > sanbi-uwc > assess_poliovirus_alignment

diff assess_alignment.py @ 7:9fd6dde72d2e draft

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planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
author sanbi-uwc
date Wed, 14 Sep 2022 11:11:02 +0000
parents 0e556a3f85d6
children 852e76e7d22a
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line diff
--- a/assess_alignment.py	Wed Sep 14 10:05:03 2022 +0000
+++ b/assess_alignment.py	Wed Sep 14 11:11:02 2022 +0000
@@ -184,7 +184,7 @@
             best_match_mismatch_list = mismatch_list
             best_match_quality = quality
             best_match_reference = dataset_name
-            best_consensus = args.consensi[file_index]
+            best_consensus = open(args.consensi[file_index]).read()
             percent_mismatches = round(min_mismatches / lengths[best_match_reference] * 100, 2)
 
     info = {