added test that actually contains plof row

PMBio · May 16, 2024 · 835b7b7 · 835b7b7
1 parent e03876d
commit 835b7b7
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Showing 4 changed files with 71 additions and 0 deletions.
diff --git a/tests/annotations/test_annotations.py b/tests/annotations/test_annotations.py
@@ -629,6 +629,12 @@ def test_filter_by_exon_distance(
             "annotations.parquet",
             "expected.parquet",
         ),
+        (
+            "select_rename_fill_columns_plof2",
+            "annotation_colnames_filling_values.yaml",
+            "annotations.parquet",
+            "expected.parquet",
+        ),
     ],
 )
 def test_select_rename_fill_annotations(

diff --git a/...ata/select_rename_fill_columns/select_rename_fill_columns_plof2/expected/expected.parquet b/...ata/select_rename_fill_columns/select_rename_fill_columns_plof2/expected/expected.parquet
diff --git a/...ll_columns/select_rename_fill_columns_plof2/input/annotation_colnames_filling_values.yaml b/...ll_columns/select_rename_fill_columns_plof2/input/annotation_colnames_filling_values.yaml
@@ -0,0 +1,65 @@
+annotation_column_names: 
+  'af' : 
+    'combined_UKB_NFE_AF' : 0
+  'maf_mb' : 
+    'combined_UKB_NFE_AF_MB' : 10000
+  'maf' :
+    'combined_UKB_NFE_MAF' : 0
+  'PolyPhen' : 
+    'polyphen_score' : 0
+  'SIFT' : 
+    'sift_score' : 1
+  'QKI_hg2' : 
+    'DeepRipe_plus_QKI_lip_hg2' : 0
+  'QKI_k5' : 
+    'DeepRipe_plus_QKI_clip_k5' : 0
+  'KHDRBS1_k5' : 
+    'DeepRipe_plus_KHDRBS1_clip_k5' : 0
+  'ELAVL1_parclip' : 
+    'DeepRipe_plus_ELAVL1_parclip' : 0
+  'TARDBP_parclip' : 
+    'DeepRipe_plus_TARDBP_parclip' : 0
+  'HNRNPD_parclip' : 
+    'DeepRipe_plus_HNRNPD_parclip' : 0
+  'MBNL1_parclip' : 
+    'DeepRipe_plus_MBNL1_parclip' : 0
+  'QKI_parclip' : 
+    'DeepRipe_plus_QKI_parclip' : 0
+  'Consequence_splice_acceptor_variant' :
+    'Consequence_splice_acceptor_variant' : 0
+  'Consequence_splice_donor_variant' :
+    'Consequence_splice_donor_variant' : 0
+  'Consequence_stop_gained' :
+    'Consequence_stop_gained' : 0
+  'Consequence_frameshift_variant' :
+    'Consequence_frameshift_variant' : 0
+  'Consequence_stop_lost' :
+    'Consequence_stop_lost' : 0
+  'Consequence_start_lost' :
+    'Consequence_start_lost' : 0
+  'Consequence_inframe_insertion' :
+    'Consequence_inframe_insertion' : 0
+  'Consequence_inframe_deletion' :
+    'Consequence_inframe_deletion' : 0
+  'Consequence_missense_variant' :
+    'Consequence_missense_variant' : 0
+  'Consequence_protein_altering_variant' :
+    'Consequence_protein_altering_variant' : 0
+  'Consequence_splice_region_variant' :
+    'Consequence_splice_region_variant' : 0
+  'DeepSEA_PC_1' :
+    'DeepSEA_PC_1' : 0
+  'DeepSEA_PC_2' :
+    'DeepSEA_PC_2' : 0
+  'DeepSEA_PC_3' :
+    'DeepSEA_PC_3' : 0
+  'DeepSEA_PC_4' :
+    'DeepSEA_PC_4' : 0
+  'DeepSEA_PC_5' :
+    'DeepSEA_PC_5' : 0
+  'DeepSEA_PC_6' :
+    'DeepSEA_PC_6' : 0
+  'AF' :
+    'AF' : 0
+  'is_plof':
+    'is_plof' : 0
diff --git a/...ata/select_rename_fill_columns/select_rename_fill_columns_plof2/input/annotations.parquet b/...ata/select_rename_fill_columns/select_rename_fill_columns_plof2/input/annotations.parquet