explicitly check p1 and p2 not misassigned

cov-lineages · Feb 23, 2021 · 63a94b3 · 63a94b3
1 parent 1763ac0
commit 63a94b3
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diff --git 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
@@ -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
@@ -1,3 +1,4 @@
+#!/usr/bin/env python3
 import imp
 import argparse
 from collections import defaultdict