feat: remove non-GISAID strainnames in deduplicate scripts

Thanks @AngieHinrichs for the suggestion in 10404d2#commitcomment-105766629
cov-lineages · Mar 23, 2023 · 367c6fb · 367c6fb · AngieHinrichs · Mar 23, 2023
1 parent 034686c
commit 367c6fb
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diff --git a/deduplicate_keeping_first.py b/deduplicate_keeping_first.py
@@ -27,6 +27,13 @@
         d.remove(current)
         print(f"Removed duplicate strain: {line}")
         continue
+    # Exclude strain names that are not GISAIDy
+    # strain names must have at least 2 slashes
+    # This gets rid of things like `strain` or `OX0123456`
+    if split[0].count('/') < 2 and line != 'taxon,lineage\n':
+        d.remove(current)
+        print(f"Removed non-GISAID strain: {line}")
+        continue
     hashset.add(split[0])
 
 

diff --git a/deduplicate_keeping_last.py b/deduplicate_keeping_last.py
@@ -27,6 +27,13 @@
         d.remove(current)
         print(f"Removed duplicate strain: {line}")
         continue
+    # Exclude strain names that are not GISAIDy
+    # strain names must have at least 2 slashes
+    # This gets rid of things like `strain` or `OX0123456`
+    if split[0].count('/') < 2 and line != 'taxon,lineage\n':
+        d.remove(current)
+        print(f"Removed non-GISAID strain: {line}")
+        continue
     hashset.add(split[0])