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added Nextclade's pangolin assigment to datatables
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- can be interessting when waiting for pangolin-data updates
- not added it the HTML report
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MarieLataretu authored Jan 18, 2024
1 parent 525645a commit 9d94f51
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion bin/summary_report.py
Original file line number Diff line number Diff line change
Expand Up @@ -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'])
Expand All @@ -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']]
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