From 4ddde29ee36747f32223df2c1bd67767e8d42df1 Mon Sep 17 00:00:00 2001
From: jkgoodrich <33063077+jkgoodrich@users.noreply.github.com>
Date: Thu, 19 Dec 2024 10:59:29 -0700
Subject: [PATCH 1/2] Use `parse_variant` in gnomad_methods

---
 gnomad_toolbox/filtering/variant.py | 19 ++++---------------
 requirements.txt                    |  3 ++-
 setup.py                            |  2 +-
 3 files changed, 7 insertions(+), 17 deletions(-)

diff --git a/gnomad_toolbox/filtering/variant.py b/gnomad_toolbox/filtering/variant.py
index ec00bc7..0de3172 100644
--- a/gnomad_toolbox/filtering/variant.py
+++ b/gnomad_toolbox/filtering/variant.py
@@ -3,6 +3,7 @@
 from typing import Optional, Union
 
 import hail as hl
+from gnomad.utils.parse import parse_variant
 from gnomad.utils.reference_genome import get_reference_genome
 
 from gnomad_toolbox.load_data import _get_gnomad_release
@@ -47,21 +48,8 @@ def get_single_variant(
     # Determine the reference genome build for the ht.
     build = get_reference_genome(ht.locus).name
 
-    # TODO: Move this to gnomad_methods.
-    # Parse the variant string if provided.
-    try:
-        if variant and ":" not in variant:
-            contig, position, ref, alt = variant.split("-")
-        if all([contig, position, ref, alt]):
-            variant = f"{contig}:{position}:{ref}:{alt}"
-        variant = hl.eval(hl.parse_variant(variant, reference_genome=build))
-    except ValueError:
-        raise ValueError(
-            f"Invalid variant format: {variant}. Expected format: chr12-235245-A-C "
-            f"or chr12:235245:A:C"
-        )
-
     # Filter to the Locus of the variant of interest.
+    variant = parse_variant(variant, contig, position, ref, alt, build)
     ht = hl.filter_intervals(
         ht, [hl.interval(variant.locus, variant.locus, includes_end=True)]
     )
@@ -72,7 +60,8 @@ def get_single_variant(
     # Check if the variant exists.
     if ht.count() == 0:
         hl.utils.warning(
-            f"No variant found at {variant.locus} with alleles {variant.alleles}"
+            f"No variant found at {hl.eval(variant.locus)} with alleles "
+            f"{hl.eval(variant.alleles)}"
         )
 
     return ht
diff --git a/requirements.txt b/requirements.txt
index 32706b5..3410cd0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,6 @@
 # We're using the main branch of gnomad_method on github rather than the pip version
-git+https://github.com/broadinstitute/gnomad_methods@main
+# TODO: Decide on how to handle this. We might just need to have more releases of gnomad_methods.
+#git+https://github.com/broadinstitute/gnomad_methods@main
 hail
 jupyter
 jupyter_contrib_nbextensions
diff --git a/setup.py b/setup.py
index 8bc0d5d..78ab1cb 100644
--- a/setup.py
+++ b/setup.py
@@ -21,7 +21,7 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/broadinstitute/gnomad-toolbox",
-    packages=setuptools.find_namespace_packages(include=["gnomad_toolbox.*"]),
+    packages=setuptools.find_namespace_packages(include=["gnomad_toolbox*"]),
     project_urls={
         "Documentation": "https://broadinstitute.github.io/gnomad-toolbox/",
         "Source Code": "https://github.com/broadinstitute/gnomad-toolbox",

From e542c1b70fd1e1718f7159a1d3f8d8f482407de5 Mon Sep 17 00:00:00 2001
From: jkgoodrich <33063077+jkgoodrich@users.noreply.github.com>
Date: Thu, 19 Dec 2024 11:56:37 -0700
Subject: [PATCH 2/2] Uncomment

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 3410cd0..702bdab 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
 # We're using the main branch of gnomad_method on github rather than the pip version
 # TODO: Decide on how to handle this. We might just need to have more releases of gnomad_methods.
-#git+https://github.com/broadinstitute/gnomad_methods@main
+git+https://github.com/broadinstitute/gnomad_methods@main
 hail
 jupyter
 jupyter_contrib_nbextensions