Add pext and constraint resources

gnomad/resources/grch37/gnomad.py

@@ -104,6 +104,29 @@ def _liftover_data_path(data_type: str, version: str) -> str:
     return f"gs://gnomad-public-requester-pays/release/{version}/liftover_grch38/ht/{data_type}/gnomad.{data_type}.r{version}.sites.liftover_grch38.ht"
 
 
+def _public_constraint_ht_path(version: str) -> str:
+    """
+    Get public constraint table path.
+
+    :param version: One of the release versions of gnomAD on GRCh38
+    :return: Path to constraint Table
+    """
+    return f"gs://gnomad-public-requester-pays/release/{version}/constraint/gnomad.v{version}.lof_metrics.by_transcript.ht"
+
+
+def _public_pext_path(data_format: str) -> str:
+    """
+    Get public pext data.
+
+    :param data_format: Either "tsv" or "ht".
+    :return: Path to pext data.
+    """
+    # TODO: Could you confirm if this is correct path?
+    if data_format not in ["tsv.gz", "ht"]:
+        raise DataException(f"{data_format} not in ['tsv.gz', 'ht']")
+    return f"gs://gnomad-public-requester-pays/papers/2019-tx-annotation/gnomad_browser/all.baselevel.021620.{data_format}"
+
+
 def public_release(data_type: str) -> VersionedTableResource:
     """
     Retrieve publicly released versioned table resource.
@@ -219,3 +242,31 @@ def release_vcf_path(data_type: str, version: str, contig: str) -> str:
 
     contig = f".{contig}" if contig else ""
     return f"gs://gcp-public-data--gnomad/release/{version}/vcf/{data_type}/gnomad.{data_type}.r{version}.sites{contig}.vcf.bgz"
+
+
+def pext() -> GnomadPublicTableResource:
+    """
+    Retrieve pext data.
+
+    :return: Pext Table
+    """
+    return GnomadPublicTableResource(path=_public_pext_path("ht"))
+
+
+def constraint() -> VersionedTableResource:
+    """
+    Retrieve constraint table.
+
+    :param version: One of the release versions of gnomAD on GRCh38
+    :return: Constraint Table
+    """
+    current_release = CURRENT_EXOME_RELEASE
+    releases = EXOME_RELEASES
+
+    return VersionedTableResource(
+        current_release,
+        {
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
+            for release in releases
+        },
+    )

gnomad/resources/grch38/gnomad.py

@@ -46,6 +46,7 @@
 MAJOR_RELEASES = ["v3", "v4"]
 CURRENT_MAJOR_RELEASE = MAJOR_RELEASES[-1]
 
+CURRENT_GTEX_RELEASE = "v10"
 
 GENOME_POPS = ["AFR", "AMI", "AMR", "ASJ", "EAS", "FIN", "NFE", "SAS", "OTH"]
 SUBSETS = {
@@ -365,6 +366,28 @@ def _public_an_ht_path(data_type: str, version: str) -> str:
     return f"gs://gnomad-public-requester-pays/release/{version}/ht/{data_type}/gnomad.{data_type}.v{version}.allele_number_all_sites.ht"
 
 
+def _public_pext_ht_path(type: str, version: str, gtex_versioin: str) -> str:
+    """
+    Get public pext hail table.
+
+    :param type: One of "base_level" or "annotation_level"
+    :param version: The gnomAD version used to generate pext.
+    :param gtex_version: The GTEx version used to generate pext
+    :return: Path to pext Table
+    """
+    return f"gs://gnomad-public-requester-pays/release/{version}/pext/gnomad.pext.gtex_{gtex_versioin}.{type}.ht"
+
+
+def _public_constraint_ht_path(version: str) -> str:
+    """
+    Get public constraint table path.
+
+    :param version: One of the release versions of gnomAD on GRCh38
+    :return: Path to constraint Table
+    """
+    return f"gs://gnomad-public-requester-pays/release/{version}/constraint/gnomad.v{version}.constraint_metrics.ht"
+
+
 def public_release(data_type: str) -> VersionedTableResource:
     """
     Retrieve publicly released versioned table resource.
@@ -701,3 +724,50 @@ def gnomad_gks(
         outputs.append(out)
 
     return outputs
+
+
+def pext(type: str, gtex_version: str = CURRENT_GTEX_RELEASE) -> VersionedTableResource:
+    """
+    Retrieve pext table by type.
+
+    :param type: One of "base_level" or "annotation_level".
+    :param gtex_version: The GTEx version used to generate P
+    :return: Pext Table.
+    """
+    if type not in ["base_level", "annotation_level"]:
+        raise DataException(
+            f"{type} not in ['base_level', 'annotation_level'], please select a type from"
+            f" ['base_level', 'annotation_level']"
+        )
+
+    current_release = CURRENT_EXOME_RELEASE
+    releases = EXOME_RELEASES
+
+    return VersionedTableResource(
+        current_release,
+        {
+            release: GnomadPublicTableResource(
+                path=_public_pext_ht_path(type, release, gtex_version)
+            )
+            for release in releases
+        },
+    )
+
+
+def constraint() -> VersionedTableResource:
+    """
+    Retrieve constraint table.
+
+    :param version: One of the release versions of gnomAD on GRCh38
+    :return: Constraint Table
+    """
+    current_release = CURRENT_EXOME_RELEASE
+    releases = EXOME_RELEASES
+
+    return VersionedTableResource(
+        current_release,
+        {
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
+            for release in releases
+        },
+    )