Speed increase gget enrichr and archs4 with Ensembl IDs

pachterlab · Nov 11, 2022 · 7f2da4f · 7f2da4f
1 parent 97705c3
commit 7f2da4f
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/gget/__init__.py b/gget/__init__.py
@@ -20,6 +20,6 @@
 # Mute numexpr threads info
 logging.getLogger("numexpr").setLevel(logging.WARNING)
 
-__version__ = "0.3.12"
+__version__ = "0.3.13"
 __author__ = "Laura Luebbert"
 __email__ = "[email protected]"
diff --git a/gget/gget_archs4.py b/gget/gget_archs4.py
@@ -71,8 +71,8 @@ def archs4(
     if ensembl:
         # Remove version number if passed
         gene = gene.split(".")[0]
-        
-        info_df = info(gene, verbose=False)
+
+        info_df = info(gene, verbose=False, ensembl_only=True)
 
         # Check if Ensembl ID was found
         if isinstance(info_df, type(None)):

diff --git a/gget/gget_enrichr.py b/gget/gget_enrichr.py
@@ -30,7 +30,7 @@ def enrichr(
     database,
     ensembl=False,
     plot=False,
-    figsize=(10,10),
+    figsize=(10, 10),
     ax=None,
     json=False,
     save=False,
@@ -110,11 +110,12 @@ def enrichr(
         logging.info("Getting gene symbols from Ensembl IDs.")
 
         genes_v2 = []
+
         for gene_id in genes:
             # Remove version number if passed
             gene_id = gene_id.split(".")[0]
 
-            info_df = info(gene_id, verbose=False)
+            info_df = info(gene_id, ensembl_only=True, verbose=False)
 
             # Check if Ensembl ID was found
             if isinstance(info_df, type(None)):