Merge branch 'dev' into dc_finemapper_config

opentargets · Apr 24, 2024 · 6c4ff6a · 6c4ff6a
2 parents e07b99d + e2f8e87
commit 6c4ff6a
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Showing 4 changed files with 13 additions and 13 deletions.
diff --git a/config/step/ot_variant_index.yaml b/config/step/ot_variant_index.yaml
@@ -2,5 +2,5 @@ defaults:
   - variant_index
 
 variant_annotation_path: ${datasets.variant_annotation}
-credible_set_path: ${datasets.study_locus}
+credible_set_path: ${datasets.credible_set}
 variant_index_path: ${datasets.variant_index}
diff --git a/src/airflow/dags/genetics_etl.py b/src/airflow/dags/genetics_etl.py
@@ -35,16 +35,16 @@
     # PICS credible sets from GWAS Catalog curated associations:
     "gwas_catalog_curated_credible_set": {
         "source_bucket": GWAS_CATALOG_BUCKET_NAME,
-        "source_object": "credible_set_datasets/gwas_catalog_curated",
+        "source_object": "credible_set_datasets/gwas_catalog_PICSed_curated_associations",
         "destination_bucket": RELEASE_BUCKET_NAME,
-        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/gwas_catalog_pics_from_curation",
+        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/gwas_catalog_PICSed_curated_associations",
     },
     # PICS credible sets from GWAS Catalog summary statistics:
     "gwas_catalog_sumstats_credible_set": {
         "source_bucket": GWAS_CATALOG_BUCKET_NAME,
-        "source_object": "credible_set_datasets/gwas_catalog_summary_stats",
+        "source_object": "credible_set_datasets/gwas_catalog_PICSed_summary_statistics",
         "destination_bucket": RELEASE_BUCKET_NAME,
-        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/gwas_catalog_pics_from_summary_statistics",
+        "destination_object": f"releases/{RELEASE_VERSION}/credible_set/gwas_catalog_PICSed_summary_statistics",
     },
     # GWAS Catalog manifest files:
     "gwas_catalog_manifests": {

diff --git a/src/airflow/dags/gwas_catalog_preprocess.py b/src/airflow/dags/gwas_catalog_preprocess.py
@@ -45,12 +45,8 @@
 WINDOW_BASED_CLUMPED = f"gs://{GWAS_CATALOG_BUCKET_NAME}/study_locus_datasets/gwas_catalog_summary_stats_window_clumped"
 LD_BASED_CLUMPED = f"gs://{GWAS_CATALOG_BUCKET_NAME}/study_locus_datasets/gwas_catalog_summary_stats_ld_clumped"
 # Credible sets:
-CURATED_CREDIBLE_SETS = (
-    f"gs://{GWAS_CATALOG_BUCKET_NAME}/credible_set_datasets/gwas_catalog_curated"
-)
-SUMMARY_STATISTICS_CREDIBLE_SETS = (
-    f"gs://{GWAS_CATALOG_BUCKET_NAME}/credible_set_datasets/gwas_catalog_summary_stats"
-)
+CURATED_CREDIBLE_SETS = f"gs://{GWAS_CATALOG_BUCKET_NAME}/credible_set_datasets/gwas_catalog_PICSed_curated_associations"
+SUMMARY_STATISTICS_CREDIBLE_SETS = f"gs://{GWAS_CATALOG_BUCKET_NAME}/credible_set_datasets/gwas_catalog_PICSed_summary_statistics"
 
 
 def upload_harmonized_study_list(

diff --git a/src/gentropy/pics.py b/src/gentropy/pics.py
@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from gentropy.common.session import Session
-from gentropy.dataset.study_locus import StudyLocus
+from gentropy.dataset.study_locus import CredibleInterval, StudyLocus
 from gentropy.method.pics import PICS
 
 
@@ -28,6 +28,10 @@ def __init__(
             session, study_locus_ld_annotated_in
         )
         # PICS
-        picsed_sl = PICS.finemap(study_locus_ld_annotated).annotate_credible_sets()
+        picsed_sl = (
+            PICS.finemap(study_locus_ld_annotated)
+            .annotate_credible_sets()
+            .filter_credible_set(credible_interval=CredibleInterval.IS99)
+        )
         # Write
         picsed_sl.df.write.mode(session.write_mode).parquet(picsed_study_locus_out)