From eb683fffebd9b2d0972fb9d2ee86552f5fe762e4 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 11 Dec 2024 14:40:19 -0500
Subject: [PATCH 01/15] Add pext resources

---
 gnomad/resources/grch38/gnomad.py | 39 +++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index 62cb950bb..de3383cce 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/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 = {
@@ -364,6 +365,17 @@ 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_release(data_type: str) -> VersionedTableResource:
     """
@@ -701,3 +713,30 @@ 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
+        },
+    )

From 66a934fdef507962c99f087b4adcc73a2294e580 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 11 Dec 2024 14:44:12 -0500
Subject: [PATCH 02/15] Black formatting

---
 gnomad/resources/grch38/gnomad.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index de3383cce..eb71d6461 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -365,6 +365,7 @@ 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.
@@ -374,7 +375,7 @@ def _public_pext_ht_path(type: str, version: str, gtex_versioin: str) -> str:
     :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")
+    return f"gs://gnomad-public-requester-pays/release/{version}/pext/gnomad.pext.gtex_{gtex_versioin}.{type}.ht"
 
 
 def public_release(data_type: str) -> VersionedTableResource:
@@ -714,6 +715,7 @@ def gnomad_gks(
 
     return outputs
 
+
 def pext(type: str, gtex_version: str = CURRENT_GTEX_RELEASE) -> VersionedTableResource:
     """
     Retrieve pext table by type.

From a2485a05b082fb3fe0abc3d10c1161e8150a0ee0 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Thu, 12 Dec 2024 13:48:21 -0500
Subject: [PATCH 03/15] Add constraint resources

---
 gnomad/resources/grch37/gnomad.py | 28 ++++++++++++++++++++++++++++
 gnomad/resources/grch38/gnomad.py | 29 +++++++++++++++++++++++++++++
 2 files changed, 57 insertions(+)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index cf933ed68..2d73799da 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -103,6 +103,14 @@ 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_release(data_type: str) -> VersionedTableResource:
     """
@@ -219,3 +227,23 @@ 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 constraint(version: str = CURRENT_EXOME_RELEASE) -> 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
+        },
+    )
diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index eb71d6461..ec7999c0c 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -377,6 +377,15 @@ def _public_pext_ht_path(type: str, version: str, gtex_versioin: str) -> str:
     """
     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:
     """
@@ -742,3 +751,23 @@ def pext(type: str, gtex_version: str = CURRENT_GTEX_RELEASE) -> VersionedTableR
             for release in releases
         },
     )
+
+def constraint(version: str = CURRENT_EXOME_RELEASE) -> 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
+        },
+    )

From 0e7f3e73cb1063b99452de6b3c3fbed251fecefb Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Thu, 12 Dec 2024 13:48:39 -0500
Subject: [PATCH 04/15] Add constraint resources

---
 gnomad/resources/grch37/gnomad.py | 9 +++++----
 gnomad/resources/grch38/gnomad.py | 8 ++++----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index 2d73799da..46435968c 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -103,6 +103,7 @@ 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.
@@ -110,7 +111,8 @@ def _public_constraint_ht_path(version: str) -> str:
     :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")
+    return f"gs://gnomad-public-requester-pays/release/{version}/constraint/gnomad.v{version}.lof_metrics.by_transcript.ht"
+
 
 def public_release(data_type: str) -> VersionedTableResource:
     """
@@ -228,6 +230,7 @@ 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 constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     """
     Retrieve constraint table.
@@ -241,9 +244,7 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     return VersionedTableResource(
         current_release,
         {
-            release: GnomadPublicTableResource(
-                path=_public_constraint_ht_path(release)
-            )
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
             for release in releases
         },
     )
diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index ec7999c0c..58b1f7a3b 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -377,6 +377,7 @@ def _public_pext_ht_path(type: str, version: str, gtex_versioin: str) -> str:
     """
     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.
@@ -384,7 +385,7 @@ def _public_constraint_ht_path(version: str) -> str:
     :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")
+    return f"gs://gnomad-public-requester-pays/release/{version}/constraint/gnomad.v{version}.constraint_metrics.ht"
 
 
 def public_release(data_type: str) -> VersionedTableResource:
@@ -752,6 +753,7 @@ def pext(type: str, gtex_version: str = CURRENT_GTEX_RELEASE) -> VersionedTableR
         },
     )
 
+
 def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     """
     Retrieve constraint table.
@@ -765,9 +767,7 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     return VersionedTableResource(
         current_release,
         {
-            release: GnomadPublicTableResource(
-                path=_public_constraint_ht_path(release)
-            )
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
             for release in releases
         },
     )

From f69f6484ae2bd749ca17a69ea57d869f10337425 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Thu, 12 Dec 2024 14:05:59 -0500
Subject: [PATCH 05/15] Add pext for GRCh37

---
 gnomad/resources/grch37/gnomad.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index 46435968c..11aafea96 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -113,6 +113,18 @@ def _public_constraint_ht_path(version: str) -> str:
     """
     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:
     """
@@ -230,6 +242,13 @@ 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(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     """

From 4a41c7eb6abfc0d55ea72dd91f2d4535d7aff919 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Thu, 12 Dec 2024 14:06:18 -0500
Subject: [PATCH 06/15] Add pext for GRCh37

---
 gnomad/resources/grch37/gnomad.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index 11aafea96..2c4ca332a 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -113,6 +113,7 @@ def _public_constraint_ht_path(version: str) -> str:
     """
     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.
@@ -123,7 +124,7 @@ def _public_pext_path(data_format: str) -> str:
     # 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}")
+    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:
@@ -242,13 +243,15 @@ 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'))
+    return GnomadPublicTableResource(path=_public_pext_path("ht"))
+
 
 def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     """

From ddcab90770baeed933c5ebc679cf5417c5ad304f Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Thu, 12 Dec 2024 14:14:24 -0500
Subject: [PATCH 07/15] fix unused argument

---
 gnomad/resources/grch37/gnomad.py | 2 +-
 gnomad/resources/grch38/gnomad.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index 2c4ca332a..d39645aac 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -266,7 +266,7 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     return VersionedTableResource(
         current_release,
         {
-            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(version))
             for release in releases
         },
     )
diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index 58b1f7a3b..d9ff6657c 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -767,7 +767,7 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     return VersionedTableResource(
         current_release,
         {
-            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(version))
             for release in releases
         },
     )

From 149b9d9502092ff90f4191b4981b47dcb2b84a4a Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Thu, 12 Dec 2024 14:29:52 -0500
Subject: [PATCH 08/15] Make it default to current release

---
 gnomad/resources/grch37/gnomad.py | 4 ++--
 gnomad/resources/grch38/gnomad.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index d39645aac..a514023c6 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -253,7 +253,7 @@ def pext() -> GnomadPublicTableResource:
     return GnomadPublicTableResource(path=_public_pext_path("ht"))
 
 
-def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
+def constraint() -> VersionedTableResource:
     """
     Retrieve constraint table.
 
@@ -266,7 +266,7 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     return VersionedTableResource(
         current_release,
         {
-            release: GnomadPublicTableResource(path=_public_constraint_ht_path(version))
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
             for release in releases
         },
     )
diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index d9ff6657c..0ea7932e0 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -754,7 +754,7 @@ def pext(type: str, gtex_version: str = CURRENT_GTEX_RELEASE) -> VersionedTableR
     )
 
 
-def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
+def constraint() -> VersionedTableResource:
     """
     Retrieve constraint table.
 
@@ -767,7 +767,7 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     return VersionedTableResource(
         current_release,
         {
-            release: GnomadPublicTableResource(path=_public_constraint_ht_path(version))
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
             for release in releases
         },
     )

From 78bd2f541ac3ab4e6b8e88959e8e86de763d4af2 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 11:56:53 -0500
Subject: [PATCH 09/15] Address review suggestions

---
 gnomad/resources/grch37/gnomad.py | 44 +++++++++++--------------------
 1 file changed, 15 insertions(+), 29 deletions(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index a514023c6..c959319ce 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -104,27 +104,22 @@ 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:
+def _public_constraint_ht_path() -> str:
     """
-    Get public constraint table path.
+    Get public gene constraint Table path.
 
-    :param version: One of the release versions of gnomAD on GRCh38
-    :return: Path to constraint Table
+    :return: Path to constraint Table.
     """
-    return f"gs://gnomad-public-requester-pays/release/{version}/constraint/gnomad.v{version}.lof_metrics.by_transcript.ht"
+    return f"gs://gnomad-public-requester-pays/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.ht"
 
 
-def _public_pext_path(data_format: str) -> str:
+def _public_pext_path() -> str:
     """
-    Get public pext data.
+    Get public proportion expressed across transcripts (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}"
+    return (f"gs://gnomad-public-requester-pays/papers/2019-tx-annotation/gnomad_browser/all.baselevel.021620.ht")
 
 
 def public_release(data_type: str) -> VersionedTableResource:
@@ -246,27 +241,18 @@ def release_vcf_path(data_type: str, version: str, contig: str) -> str:
 
 def pext() -> GnomadPublicTableResource:
     """
-    Retrieve pext data.
+    Retrieve proportion expressed across transcripts (pext) data.
 
-    :return: Pext Table
+    :return: Pext Table.
     """
-    return GnomadPublicTableResource(path=_public_pext_path("ht"))
+    return GnomadPublicTableResource(path=_public_pext_path())
 
 
-def constraint() -> VersionedTableResource:
+def constraint() -> GnomadPublicTableResource:
     """
-    Retrieve constraint table.
+    Retrieve gene constraint table.
 
-    :param version: One of the release versions of gnomAD on GRCh38
-    :return: Constraint Table
+    :param version: One of the release versions of gnomAD on GRCh37.
+    :return: Gene 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
-        },
-    )
+    return GnomadPublicTableResource(path=_public_constraint_ht_path())

From 0c021f476a62a82c71e33ab238d4d18ecdad4309 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 12:13:32 -0500
Subject: [PATCH 10/15] Black formatting

---
 gnomad/resources/grch37/gnomad.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index c959319ce..07d6e72eb 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -119,7 +119,7 @@ def _public_pext_path() -> str:
 
     :return: Path to pext data.
     """
-    return (f"gs://gnomad-public-requester-pays/papers/2019-tx-annotation/gnomad_browser/all.baselevel.021620.ht")
+    return f"gs://gnomad-public-requester-pays/papers/2019-tx-annotation/gnomad_browser/all.baselevel.021620.ht"
 
 
 def public_release(data_type: str) -> VersionedTableResource:

From 384920d2c8d9a6f1f606b827a4d058e584a6aa89 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:21:56 -0500
Subject: [PATCH 11/15] Address review comments

---
 gnomad/resources/grch37/gnomad.py | 23 +++++++---
 gnomad/resources/grch38/gnomad.py | 70 ++++++++++++++-----------------
 2 files changed, 49 insertions(+), 44 deletions(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index 07d6e72eb..c1af4ca4e 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -113,13 +113,26 @@ def _public_constraint_ht_path() -> str:
     return f"gs://gnomad-public-requester-pays/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.ht"
 
 
-def _public_pext_path() -> str:
+def _public_pext_path(pext_type: str = "base_level") -> str:
     """
     Get public proportion expressed across transcripts (pext) data.
 
+    :param pext_type: One of "annotation_level" or "base_level". Default is "base_level".
     :return: Path to pext data.
+    :raises DataException: If the provided pext_type is invalid.
     """
-    return f"gs://gnomad-public-requester-pays/papers/2019-tx-annotation/gnomad_browser/all.baselevel.021620.ht"
+    pext_paths = {
+        "annotation_level": "gs://gnomad-public-requester-pays/papers/2019-tx-annotation/pre_computed/all.possible.snvs.tx_annotated.021520.ht",
+        "base_level": "gs://gnomad-public-requester-pays/papers/2019-tx-annotation/gnomad_browser/all.baselevel.021620.ht",
+    }
+
+    if pext_type not in pext_paths:
+        valid_types = list(pext_paths.keys())
+        raise DataException(
+            f"Invalid pext_type: '{pext_type}'. Valid options are {valid_types}."
+        )
+
+    return pext_paths[pext_type]
 
 
 def public_release(data_type: str) -> VersionedTableResource:
@@ -239,20 +252,20 @@ def release_vcf_path(data_type: str, version: str, contig: str) -> str:
     return f"gs://gcp-public-data--gnomad/release/{version}/vcf/{data_type}/gnomad.{data_type}.r{version}.sites{contig}.vcf.bgz"
 
 
-def pext() -> GnomadPublicTableResource:
+def pext(pext_type: str='base_level') -> GnomadPublicTableResource:
     """
     Retrieve proportion expressed across transcripts (pext) data.
 
+    :param pext_type: One of "annotation_level" or "base_level". Default is "base_level".
     :return: Pext Table.
     """
-    return GnomadPublicTableResource(path=_public_pext_path())
+    return GnomadPublicTableResource(path=_public_pext_path(pext_type))
 
 
 def constraint() -> GnomadPublicTableResource:
     """
     Retrieve gene constraint table.
 
-    :param version: One of the release versions of gnomAD on GRCh37.
     :return: Gene constraint Table.
     """
     return GnomadPublicTableResource(path=_public_constraint_ht_path())
diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index 0ea7932e0..fbd2ecc50 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -366,24 +366,29 @@ 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:
+def _public_pext_ht_path(pext_type: str='base_level') -> 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
+    :param pext_type: One of "base_level" or "annotation_level". Default is "base_level".
+    :return: Path to pext Table.
     """
-    return f"gs://gnomad-public-requester-pays/release/{version}/pext/gnomad.pext.gtex_{gtex_versioin}.{type}.ht"
+    valid_types = ["base_level", "annotation_level"]
+
+    if pext_type not in valid_types:
+        raise DataException(
+            f"Invalid pext_type: '{pext_type}'. Valid options are {valid_types}."
+        )
+
+    return f"gs://gnomad-public-requester-pays/release/4.1/pext/gnomad.pext.gtex_v10.{pext_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
+    :param version: One of the 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"
 
@@ -726,48 +731,35 @@ def gnomad_gks(
     return outputs
 
 
-def pext(type: str, gtex_version: str = CURRENT_GTEX_RELEASE) -> VersionedTableResource:
+def pext(pext_type: str='base_level') -> GnomadPublicTableResource:
     """
     Retrieve pext table by type.
 
-    :param type: One of "base_level" or "annotation_level".
-    :param gtex_version: The GTEx version used to generate P
+    :param pext_type: One of "base_level" or "annotation_level". Default is "base_level".
     :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
-        },
-    )
+    return GnomadPublicTableResource(path=_public_pext_ht_path(pext_type))
 
 
-def constraint() -> VersionedTableResource:
+def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     """
-    Retrieve constraint table.
+    Retrieve gene constraint Table.
 
-    :param version: One of the release versions of gnomAD on GRCh38
-    :return: Constraint Table
+    :param version: One of the release versions of gnomAD on GRCh38. Default is the current exome release.
+    :return: constraint Table.
+    :raises ValueError: If the version is not a valid release.
     """
+    # Validate the version
+    if version not in EXOME_RELEASES:
+        raise ValueError(f"Invalid version: {version}. Must be one of {EXOME_RELEASES}.")
+
     current_release = CURRENT_EXOME_RELEASE
     releases = EXOME_RELEASES
 
     return VersionedTableResource(
-        current_release,
-        {
-            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
-            for release in releases
-        },
-    )
+            current_release,
+            {
+                release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
+                for release in releases
+            },
+        )

From 7f97ab00350a2c244b2e90337df46944f454d402 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:22:10 -0500
Subject: [PATCH 12/15] Address review comments

---
 gnomad/resources/grch37/gnomad.py |  2 +-
 gnomad/resources/grch38/gnomad.py | 20 +++++++++++---------
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index c1af4ca4e..4a1c23364 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -252,7 +252,7 @@ def release_vcf_path(data_type: str, version: str, contig: str) -> str:
     return f"gs://gcp-public-data--gnomad/release/{version}/vcf/{data_type}/gnomad.{data_type}.r{version}.sites{contig}.vcf.bgz"
 
 
-def pext(pext_type: str='base_level') -> GnomadPublicTableResource:
+def pext(pext_type: str = "base_level") -> GnomadPublicTableResource:
     """
     Retrieve proportion expressed across transcripts (pext) data.
 
diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index fbd2ecc50..2d6f6c2f5 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -366,7 +366,7 @@ 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(pext_type: str='base_level') -> str:
+def _public_pext_ht_path(pext_type: str = "base_level") -> str:
     """
     Get public pext hail table.
 
@@ -731,7 +731,7 @@ def gnomad_gks(
     return outputs
 
 
-def pext(pext_type: str='base_level') -> GnomadPublicTableResource:
+def pext(pext_type: str = "base_level") -> GnomadPublicTableResource:
     """
     Retrieve pext table by type.
 
@@ -751,15 +751,17 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     """
     # Validate the version
     if version not in EXOME_RELEASES:
-        raise ValueError(f"Invalid version: {version}. Must be one of {EXOME_RELEASES}.")
+        raise ValueError(
+            f"Invalid version: {version}. Must be one of {EXOME_RELEASES}."
+        )
 
     current_release = CURRENT_EXOME_RELEASE
     releases = EXOME_RELEASES
 
     return VersionedTableResource(
-            current_release,
-            {
-                release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
-                for release in releases
-            },
-        )
+        current_release,
+        {
+            release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
+            for release in releases
+        },
+    )

From f386dea1d79496c5ca29114ff5ec3bbdb77fe666 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:26:49 -0500
Subject: [PATCH 13/15] minor edit

---
 gnomad/resources/grch38/gnomad.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index 2d6f6c2f5..6267be414 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -368,7 +368,7 @@ def _public_an_ht_path(data_type: str, version: str) -> str:
 
 def _public_pext_ht_path(pext_type: str = "base_level") -> str:
     """
-    Get public pext hail table.
+    Get public proportion expressed across transcripts (pext) data.
 
     :param pext_type: One of "base_level" or "annotation_level". Default is "base_level".
     :return: Path to pext Table.
@@ -749,7 +749,6 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     :return: constraint Table.
     :raises ValueError: If the version is not a valid release.
     """
-    # Validate the version
     if version not in EXOME_RELEASES:
         raise ValueError(
             f"Invalid version: {version}. Must be one of {EXOME_RELEASES}."

From 235af442b154bec59e768cb1f94730acb6e42770 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:31:18 -0500
Subject: [PATCH 14/15] Remove unused f-string

---
 gnomad/resources/grch37/gnomad.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnomad/resources/grch37/gnomad.py b/gnomad/resources/grch37/gnomad.py
index 4a1c23364..9c9ab1a99 100644
--- a/gnomad/resources/grch37/gnomad.py
+++ b/gnomad/resources/grch37/gnomad.py
@@ -110,7 +110,7 @@ def _public_constraint_ht_path() -> str:
 
     :return: Path to constraint Table.
     """
-    return f"gs://gnomad-public-requester-pays/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.ht"
+    return "gs://gnomad-public-requester-pays/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.ht"
 
 
 def _public_pext_path(pext_type: str = "base_level") -> str:

From 3f62849597392fbefbc9417a9c64244ff3bc2355 Mon Sep 17 00:00:00 2001
From: Qin He <44242118+KoalaQin@users.noreply.github.com>
Date: Wed, 18 Dec 2024 15:25:46 -0500
Subject: [PATCH 15/15] Apply review suggestions

---
 gnomad/resources/grch38/gnomad.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/gnomad/resources/grch38/gnomad.py b/gnomad/resources/grch38/gnomad.py
index 6267be414..3403a1d14 100644
--- a/gnomad/resources/grch38/gnomad.py
+++ b/gnomad/resources/grch38/gnomad.py
@@ -46,8 +46,6 @@
 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 = {
     "v3": [
@@ -746,7 +744,7 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
     Retrieve gene constraint Table.
 
     :param version: One of the release versions of gnomAD on GRCh38. Default is the current exome release.
-    :return: constraint Table.
+    :return: Gene constraint Table.
     :raises ValueError: If the version is not a valid release.
     """
     if version not in EXOME_RELEASES:
@@ -754,13 +752,10 @@ def constraint(version: str = CURRENT_EXOME_RELEASE) -> VersionedTableResource:
             f"Invalid version: {version}. Must be one of {EXOME_RELEASES}."
         )
 
-    current_release = CURRENT_EXOME_RELEASE
-    releases = EXOME_RELEASES
-
     return VersionedTableResource(
-        current_release,
+        CURRENT_EXOME_RELEASE,
         {
             release: GnomadPublicTableResource(path=_public_constraint_ht_path(release))
-            for release in releases
+            for release in EXOME_RELEASES
         },
     )