Move species filtering for 'phage' and 'sp.'

Removed filtering of species names that include 'phage' or 'sp.' from the DataFrame.

Author: Ulthran

scripts/parse.py

@@ -94,6 +94,10 @@ def _extract_species_name(classification: str) -> str:
         )
         return ""
 
+    # Filter out classifications we don't want
+    if "phage" in species or "sp." in species:
+        return ""
+    
     return species
 
 
@@ -171,10 +175,6 @@ def parse_mash_winning_sorted_tab(
     # Extract species names
     df["species"] = df["full_classification"].apply(_extract_species_name)
 
-    # Filter out species names that include "phage"
-    df = df[~df["species"].str.contains("phage", case=False, na=False)]
-    df = df[~df["species"].str.contains("sp.", case=False, na=False)]
-
     # Filter by median multiplicity factor
     if df.empty:
         logger.debug("No mash hits after species filtering", extra={"path": str(fp)})