Build RNU4ATAC transcript patches and export to ES

Author: phildarnowsky-broad

data-pipeline/src/data_pipeline/pipelines/export_to_elasticsearch.py

@@ -42,6 +42,8 @@
 from data_pipeline.pipelines.gnomad_v4_lof_curation_results import pipeline as gnomad_v4_lof_curation_results_pipeline
 
 from data_pipeline.pipelines.gene_patches import pipeline as gnomad_v4_gene_patches
+from data_pipeline.pipelines.transcript_patches import pipeline as gnomad_v4_transcript_patches
+
 
 logger = logging.getLogger("gnomad_data_pipeline")
 
@@ -119,6 +121,17 @@ def add_liftover_document_id(ds):
             "block_size": 1_000,
         },
     },
+    "transcripts_grch38_patched": {
+        "get_table": lambda: hl.read_table(
+            gnomad_v4_transcript_patches.get_output("transcripts_grch38_patched").get_output_path()
+        ),
+        "args": {
+            "index": "transcripts_grch38_patched",
+            "index_fields": ["transcript_id"],
+            "id_field": "transcript_id",
+            "block_size": 1_000,
+        },
+    },
     ##############################################################################################################
     # gnomAD v4
     ##############################################################################################################

data-pipeline/src/data_pipeline/pipelines/transcript_patches.py

@@ -0,0 +1,28 @@
+from data_pipeline.pipeline import Pipeline, run_pipeline
+
+from data_pipeline.data_types.transcript import extract_transcripts
+from data_pipeline.helpers import annotate_table
+
+pipeline = Pipeline()
+
+pipeline.add_task(
+    "extract_patched_transcripts",
+    extract_transcripts,
+    "/transcripts/transcripts_grch38_patched_base.ht",
+    {"genes_path": "gs://gnomad-browser-data-pipeline/phil-scratch/output/genes/genes_grch38_patched.ht"},
+)
+
+pipeline.add_task(
+    "annotate_patched_transcripts",
+    annotate_table,
+    "/transcripts/transcripts_grch38_annotated_1.ht",
+    {
+        "table_path": pipeline.get_task("extract_patched_transcripts"),
+        "gnomad_constraint": "gs://gnomad-v4-data-pipeline/output/constraint/gnomad_v4_constraint.ht",
+    },
+)
+
+pipeline.set_outputs({"transcripts_grch38_patched": "annotate_patched_transcripts"})
+
+if __name__ == "__main__":
+    run_pipeline(pipeline)