From 0e258c25e1de1c32581af75bf184113c5f360567 Mon Sep 17 00:00:00 2001
From: Ben Gyori <ben.gyori@gmail.com>
Date: Thu, 23 Jan 2025 13:24:33 -0500
Subject: [PATCH] Propagate background gene sets into ORA functions

---
 src/indra_cogex/analysis/gene_analysis.py     |  6 ++++--
 src/indra_cogex/client/enrichment/discrete.py | 20 +++++++++++++++----
 2 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/indra_cogex/analysis/gene_analysis.py b/src/indra_cogex/analysis/gene_analysis.py
index 277329bb3..0f2a8aa89 100644
--- a/src/indra_cogex/analysis/gene_analysis.py
+++ b/src/indra_cogex/analysis/gene_analysis.py
@@ -80,7 +80,8 @@ def discrete_analysis(
         )
 
     if background_gene_list:
-        background_gene_ids, _ = list(parse_gene_list(background_gene_list))
+        background_genes, _ = parse_gene_list(background_gene_list)
+        background_gene_ids = list(background_genes)
     else:
         background_gene_ids = None
 
@@ -97,7 +98,8 @@ def discrete_analysis(
         if analysis_name in {"go", "wikipathways", "reactome", "phenotype"}:
             analysis_result = analysis_func(
                 client=client, gene_ids=gene_set, method=method, alpha=alpha,
-                keep_insignificant=keep_insignificant
+                keep_insignificant=keep_insignificant,
+                background_gene_ids=background_gene_ids
             )
         else:
             # Run INDRA analysis if enabled
diff --git a/src/indra_cogex/client/enrichment/discrete.py b/src/indra_cogex/client/enrichment/discrete.py
index 7a883f652..0b8c4082d 100644
--- a/src/indra_cogex/client/enrichment/discrete.py
+++ b/src/indra_cogex/client/enrichment/discrete.py
@@ -215,7 +215,9 @@ def go_ora(
         if not background_gene_ids
         else len(background_gene_ids)
     )
-    return _do_ora(get_go(client=client), query=gene_ids, count=count, **kwargs)
+    bg_genes = frozenset(background_gene_ids) if background_gene_ids else None
+    return _do_ora(get_go(client=client, background_gene_ids=bg_genes),
+                   query=gene_ids, count=count, **kwargs)
 
 
 def wikipathways_ora(
@@ -249,8 +251,10 @@ def wikipathways_ora(
         if not background_gene_ids
         else len(background_gene_ids)
     )
+    bg_genes = frozenset(background_gene_ids) if background_gene_ids else None
     return _do_ora(
-        get_wikipathways(client=client), query=gene_ids, count=count, **kwargs
+        get_wikipathways(client=client, background_gene_ids=bg_genes),
+        query=gene_ids, count=count, **kwargs
     )
 
 
@@ -285,7 +289,9 @@ def reactome_ora(
         if not background_gene_ids
         else len(background_gene_ids)
     )
-    return _do_ora(get_reactome(client=client), query=gene_ids, count=count, **kwargs)
+    bg_genes = frozenset(background_gene_ids) if background_gene_ids else None
+    return _do_ora(get_reactome(client=client, background_gene_ids=bg_genes),
+                   query=gene_ids, count=count, **kwargs)
 
 
 @autoclient()
@@ -321,8 +327,10 @@ def phenotype_ora(
         if not background_gene_ids
         else len(background_gene_ids)
     )
+    bg_genes = frozenset(background_gene_ids) if background_gene_ids else None
     return _do_ora(
-        get_phenotype_gene_sets(client=client), query=gene_ids, count=count, **kwargs
+        get_phenotype_gene_sets(client=client, background_gene_ids=bg_genes),
+        query=gene_ids, count=count, **kwargs
     )
 
 
@@ -367,11 +375,13 @@ def indra_downstream_ora(
         if not background_gene_ids
         else len(background_gene_ids)
     )
+    bg_genes = frozenset(background_gene_ids) if background_gene_ids else None
     return _do_ora(
         get_entity_to_regulators(
             client=client,
             minimum_evidence_count=minimum_evidence_count,
             minimum_belief=minimum_belief,
+            background_gene_ids=bg_genes
         ),
         query=gene_ids,
         count=count,
@@ -420,11 +430,13 @@ def indra_upstream_ora(
         if not background_gene_ids
         else len(background_gene_ids)
     )
+    bg_genes = frozenset(background_gene_ids) if background_gene_ids else None
     return _do_ora(
         get_entity_to_targets(
             client=client,
             minimum_evidence_count=minimum_evidence_count,
             minimum_belief=minimum_belief,
+            background_gene_ids=bg_genes
         ),
         query=gene_ids,
         count=count,