fix alias loading

CostaLab · Jun 25, 2021 · 59e9973 · 59e9973
1 parent 4db81bc
commit 59e9973
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Showing 2 changed files with 11 additions and 10 deletions.
diff --git a/rgt/AnnotationSet.py b/rgt/AnnotationSet.py
@@ -306,15 +306,16 @@ def load_alias_dict(self, file_name):
         # Iterating over alias file entries
         for line in alias_file:
             ll = line.strip().split("\t")
-            ensembl_id = ll[0]
-            official_name = ll[1]
-            alias_vec = ll[2].split("&")
-            self.symbol_dict[ensembl_id] = official_name
-            for e in alias_vec:
-                try:
-                    self.alias_dict[e].append(ensembl_id)
-                except Exception:
-                    self.alias_dict[e] = [ensembl_id]
+            if len(ll) > 2:
+                ensembl_id = ll[0]
+                official_name = ll[1]
+                alias_vec = ll[2].split("&")
+                self.symbol_dict[ensembl_id] = official_name
+                for e in alias_vec:
+                    try:
+                        self.alias_dict[e].append(ensembl_id)
+                    except Exception:
+                        self.alias_dict[e] = [ensembl_id]
 
         # Termination
         alias_file.close()

diff --git a/test/tdf.sh b/test/tdf.sh
@@ -24,7 +24,7 @@ fi
 
 # Run test script
 cd ${DIR}/TDF_examples/FENDRR_mm9/
-rgt-TDF promotertest -r FENDRR.fasta -de fendrr_gene_list_fold_change.txt -score -organism mm9 -rn FENDRR -o promoter_test -t FENDRR_FC/ -l 20
+rgt-TDF promotertest -r FENDRR.fasta -de fendrr_gene_list_fold_change.txt -score -organism mm9 -rn FENDRR -o promoter_test -t FENDRR_FC/ -l 15
 rgt-TDF integrate -path promoter_test
 
 cd ${DIR}/TDF_examples/MEG3_hg38/