From 5ba229f7df662e29fb320e798e27f4d32c71bb86 Mon Sep 17 00:00:00 2001
From: AtaJadidAhari <atajadidahari@gmail.com>
Date: Fri, 11 Oct 2024 17:53:24 +0200
Subject: [PATCH] set FRASER2 as default FRASER version

---
 drop/demo/config_relative.yaml |  8 ++++----
 drop/template/config.yaml      | 16 ++++++++--------
 tests/config/test_AS.py        |  2 +-
 tests/pipeline/test_AS.py      |  7 +++++--
 4 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/drop/demo/config_relative.yaml b/drop/demo/config_relative.yaml
index ad78893d..30bcbece 100755
--- a/drop/demo/config_relative.yaml
+++ b/drop/demo/config_relative.yaml
@@ -42,16 +42,16 @@ aberrantSplicing:
     keepNonStandardChrs: false
     filter: false
     minExpressionInOneSample: 20
-    quantileMinExpression: 10 
-    quantileForFiltering: 0.95 
+    quantileMinExpression: 10  
     minDeltaPsi: 0.05
     implementation: PCA
     padjCutoff: 1 
     maxTestedDimensionProportion: 6
     genesToTest: "Data/genes_to_test.yaml"
-    ### FRASER1 configuration for demo dataset
-    FRASER_version: "FRASER" 
+    ### FRASER2 configuration for demo dataset
+    FRASER_version: "FRASER2"
     deltaPsiCutoff : 0.05 
+    quantileForFiltering: 0.95
 
 mae:
     run: true
diff --git a/drop/template/config.yaml b/drop/template/config.yaml
index 5b216c10..45bee136 100644
--- a/drop/template/config.yaml
+++ b/drop/template/config.yaml
@@ -51,14 +51,14 @@ aberrantSplicing:
     padjCutoff: 0.1
     maxTestedDimensionProportion: 6
     genesToTest: null
-    ### FRASER1 configuration
-    FRASER_version: "FRASER" 
-    deltaPsiCutoff : 0.3 
-    quantileForFiltering: 0.95 
-    ### For FRASER2, use the follwing parameters instead of the 3 lines above:
-    # FRASER_version: "FRASER2"
-    # deltaPsiCutoff : 0.1
-    # quantileForFiltering: 0.75
+    ### FRASER2 configuration
+    FRASER_version: "FRASER2"
+    deltaPsiCutoff : 0.1
+    quantileForFiltering: 0.75
+    ### For FRASER1, use the follwing parameters instead of the 3 lines above:
+    # FRASER_version: "FRASER"
+    # deltaPsiCutoff : 0.3
+    # quantileForFiltering: 0.95
 
 mae:
     run: true
diff --git a/tests/config/test_AS.py b/tests/config/test_AS.py
index 0fa09185..a6e4c1f8 100644
--- a/tests/config/test_AS.py
+++ b/tests/config/test_AS.py
@@ -18,7 +18,7 @@ def test_config(self, dropConfig,demo_dir):
             'deltaPsiCutoff': 0.05,
             'maxTestedDimensionProportion': 6,
             'genesToTest': 'Data/genes_to_test.yaml',
-            'FRASER_version': 'FRASER'
+            'FRASER_version': 'FRASER2',
         }
         assert dict_.items() <= dropConfig.AS.dict_.items()
 
diff --git a/tests/pipeline/test_AS.py b/tests/pipeline/test_AS.py
index c8cd7ac4..9da26360 100644
--- a/tests/pipeline/test_AS.py
+++ b/tests/pipeline/test_AS.py
@@ -56,6 +56,9 @@ def test_results(self, demo_dir):
         annotation = "v29"
         dataset = "fraser"
         r = run(f"wc -l {results_dir}/{annotation}/fraser/{dataset}/results_per_junction.tsv", demo_dir)
-        assert "4137" == r.stdout.split()[0] 
+        assert "980" == r.stdout.split()[0] 
         r = run(f"wc -l {results_dir}/{annotation}/fraser/{dataset}/results.tsv", demo_dir)
-        assert "310" == r.stdout.split()[0] 
+        assert "194" == r.stdout.split()[0] 
+        r = run(f"wc -l {results_dir}/{annotation}/fraser/{dataset}/results_gene_all.tsv", demo_dir)
+        assert "391" == r.stdout.split()[0]
+