patch for art's tweet about slashes breaking paths

cov-lineages · Jun 20, 2021 · e2c9c51 · e2c9c51
1 parent 7620ff0
commit e2c9c51
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/pangolin/__init__.py b/pangolin/__init__.py
@@ -1,5 +1,5 @@
 _program = "pangolin"
-__version__ = "3.1.3"
+__version__ = "3.1.4"
 
 __all__ = ["pangolearn",
     "utils"]

diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk
@@ -225,9 +225,10 @@ rule generate_report:
                             scorpio_lineage = new_row["scorpio_call"].split("+")[0].split("-like")[0]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(row['lineage'], alias_dict)
-                        if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
-                            new_row["note"] += f'; scorpio replaced lineage assignment {row["lineage"]}'
-                            new_row['lineage'] = scorpio_lineage
+                        if '/' not in scorpio_lineage:
+                            if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
+                                new_row["note"] += f'; scorpio replaced lineage assignment {row["lineage"]}'
+                                new_row['lineage'] = scorpio_lineage
 
                     writer.writerow(new_row)