fix: empty results against PDB

bioinf-mcb · Jun 5, 2024 · 09e3c75 · 09e3c75
1 parent a8ec4b3
commit 09e3c75
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Showing 2 changed files with 15 additions and 5 deletions.
diff --git a/mDeepFRI/mmseqs.py b/mDeepFRI/mmseqs.py
@@ -341,9 +341,14 @@ def from_best_matches(cls, filepath: str):
                                    delimiter="\t",
                                    encoding="utf-8",
                                    names=True)
-
-        query_file = np.unique(result_arr["query_file"])[0]
-        database = np.unique(result_arr["database_file"])[0]
+        try:
+            query_file = np.unique(result_arr["query_file"])[0]
+        except IndexError:
+            query_file = None
+        try:
+            database = np.unique(result_arr["database_file"])[0]
+        except IndexError:
+            database = None
 
         return cls(result_arr, query_file, database)
 

diff --git a/mDeepFRI/pipeline.py b/mDeepFRI/pipeline.py
@@ -102,8 +102,13 @@ def hierarchical_database_search(query_file: str,
         # store the location of the result for the next step
         db.mmseqs_result = mmseqs_results_path
 
-        # logging
-        unique_hits = np.unique(best_matches["query"])
+        # catch error if no matches to database
+        # a case from phage proteins
+        try:
+            unique_hits = np.unique(best_matches["query"])
+        except IndexError:
+            unique_hits = np.array([])
+
         if "pdb100" in db.name:
             pdb_hits = unique_hits
         else: