From 9d94f51f5e8f1290c136b3fa4e5df2617a47b5a1 Mon Sep 17 00:00:00 2001 From: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com> Date: Thu, 18 Jan 2024 12:22:33 +0100 Subject: [PATCH] added Nextclade's pangolin assigment to datatables - can be interessting when waiting for pangolin-data updates - not added it the HTML report --- bin/summary_report.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/summary_report.py b/bin/summary_report.py index 3294b46..7fbcab7 100755 --- a/bin/summary_report.py +++ b/bin/summary_report.py @@ -498,6 +498,7 @@ def add_nextclade_results(self, nextclade_results): self.add_column_raw('nextclade_clade', res_data['clade']) + self.add_column_raw('nextclade_pango', res_data["Nextclade_pango"]) # Nextclade's pangolin assigment self.add_column_raw('nextclade_mutations_nt', res_data['substitutions']) self.add_column_raw('nextclade_mutations', res_data['aaSubstitutions']) self.add_column_raw('nextclade_deletions_nt', res_data['deletions']) @@ -514,7 +515,7 @@ def add_nextclade_results(self, nextclade_results): # N information self.add_column_raw('nextclade_missing', res_data["missing"]) - + res_data['mutations_formatted'] = [m.replace(',', ', ') if type(m) == str else '-' for m in res_data['aaSubstitutions']] res_data['deletions_formatted'] = [m.replace(',', ', ') if type(m) == str else '-' for m in res_data['aaDeletions']] res_data['insertions_formatted'] = [m.replace(',', ', ') if type(m) == str else '-' for m in res_data['aaInsertions']]