diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk index 76e226e..28a7208 100644 --- a/pangolin/scripts/pangolearn.smk +++ b/pangolin/scripts/pangolearn.smk @@ -299,6 +299,13 @@ rule overwrite: new_row["probability"] = "1.0" new_row["lineage"] = "P.2" + writer.writerow(new_row) + elif row["lineage"] =="P.2" and row["taxon"] not in p2: + new_row = row + + new_row["probability"] = "1.0" + new_row["lineage"] = "B.1.1.28" + writer.writerow(new_row) elif row["taxon"] in p1: new_row = row @@ -310,6 +317,13 @@ rule overwrite: new_row["probability"] = "1.0" new_row["lineage"] = "P.1" + writer.writerow(new_row) + elif row["lineage"] =="P.1" and row["taxon"] not in p1: + new_row = row + + new_row["probability"] = "1.0" + new_row["lineage"] = "B.1.1.28" + writer.writerow(new_row) else: writer.writerow(row) diff --git a/pangolin/scripts/report_classes.py b/pangolin/scripts/report_classes.py index 2a89ada..e0bf204 100644 --- a/pangolin/scripts/report_classes.py +++ b/pangolin/scripts/report_classes.py @@ -1,3 +1,4 @@ +#!/usr/bin/env python3 import datetime as dt from collections import Counter diff --git a/pangolin/scripts/report_results.py b/pangolin/scripts/report_results.py index 48c465e..a8fbbb1 100644 --- a/pangolin/scripts/report_results.py +++ b/pangolin/scripts/report_results.py @@ -1,3 +1,4 @@ +#!/usr/bin/env python3 import imp import argparse from collections import defaultdict