Merge pull request #825 from broadinstitute/jg/add_mutation_rate_ht_resource

Add constraint release versioning and mutation rate table path functions

Author: jkgoodrich

gnomad/resources/grch38/gnomad.py

@@ -34,6 +34,8 @@
 CURRENT_EXOME_AN_RELEASE = "4.1"
 CURRENT_GENOME_AN_RELEASE = "4.1"
 
+CURRENT_CONSTRAINT_RELEASE = "4.1.1"
+
 EXOME_RELEASES = ["4.0", "4.1"]
 GENOME_RELEASES = ["3.0", "3.1", "3.1.1", "3.1.2", "4.0", "4.1"]
 JOINT_RELEASES = ["4.1"]
@@ -45,6 +47,9 @@
 EXOME_AN_RELEASES = ["4.1"]
 GENOME_AN_RELEASES = ["4.1"]
 
+CONSTRAINT_RELEASES = ["4.0", "4.1", "4.1.1"]
+CONSTRAINT_MUTATION_RATE_RELEASES = ["4.1.1"]
+
 DATA_TYPES = ["exomes", "genomes", "joint"]
 MAJOR_RELEASES = ["v3", "v4"]
 CURRENT_MAJOR_RELEASE = MAJOR_RELEASES[-1]
@@ -422,12 +427,22 @@ def _public_constraint_ht_path(version: str) -> str:
     """
     Get public constraint table path.
 
-    :param version: One of the release versions of gnomAD on GRCh38.
+    :param version: One of the constraint release versions of gnomAD on GRCh38.
     :return: Path to gene constraint Table.
     """
     return f"gs://gnomad-public-requester-pays/release/{version}/constraint/gnomad.v{version}.constraint_metrics.ht"
 
 
+def _public_constraint_mutation_rate_ht_path(version: str) -> str:
+    """
+    Get public constraint mutation rate table path.
+
+    :param version: One of the constraint mutation rate release versions of gnomAD on GRCh38.
+    :return: Path to mutation rate Table.
+    """
+    return f"gs://gnomad-public-requester-pays/release/{version}/constraint/model/gnomad.v{version}.mutation_rate.ht"
+
+
 def _public_browser_variant_ht_path(version: str) -> str:
     """
     Get public browser variant table path.
@@ -833,10 +848,27 @@ def constraint() -> VersionedTableResource:
     :return: Gene constraint Table.
     """
     return VersionedTableResource(
-        CURRENT_EXOME_RELEASE,
+        CURRENT_CONSTRAINT_RELEASE,
         {
             release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
-            for release in EXOME_RELEASES
+            for release in CONSTRAINT_RELEASES
+        },
+    )
+
+
+def constraint_mutation_rate() -> VersionedTableResource:
+    """
+    Retrieve constraint mutation rate Table.
+
+    :return: Mutation rate Table.
+    """
+    return VersionedTableResource(
+        CURRENT_CONSTRAINT_RELEASE,
+        {
+            release: GnomadPublicTableResource(
+                path=_public_constraint_mutation_rate_ht_path(release)
+            )
+            for release in CONSTRAINT_MUTATION_RATE_RELEASES
         },
     )