update path defs to point to new ensembl cache location

instituteofcancerresearch · Nov 21, 2023 · b9c1c4a · b9c1c4a
1 parent a230634
commit b9c1c4a
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/src/SOPRANO/core/objects.py b/src/SOPRANO/core/objects.py
@@ -293,7 +293,10 @@ class _GatherReferences:
     sizes_done: Set[int] = set()
 
     def _dest_directory(self, release: int):
-        return Directories.data(self.species) / f"{release}_{self.assembly}"
+        return (
+            Directories.ensembl_downloads(self.species)
+            / f"{release}_{self.assembly}"
+        )
 
     def _dest_fa_gz(self, release: int, _toplevel: bool):
         return self._dest_directory(release) / filename_from_url(

diff --git a/src/SOPRANO/utils/path_utils.py b/src/SOPRANO/utils/path_utils.py
@@ -6,7 +6,6 @@
 _SOPRANO_SCRIPTS = _SOPRANO_SRC / "scripts"
 _SOPRANO_R = _SOPRANO_SRC / "R"
 _SOPRANO_DATA = _SOPRANO_SRC / "data"
-_SOPRANO_HOMO_SAPIENS = _SOPRANO_DATA / "homo_sapiens"
 _SOPRANO_IMMUNO = _SOPRANO_SRC / "immunopeptidomes"
 _SOPRANO_IMMUNO_HUMANS = _SOPRANO_IMMUNO / "human"
 _SOPRANO_EXAMPLES = _SOPRANO_SRC / "examples"
@@ -15,6 +14,8 @@
 # Common dirs from repository root
 _SOPRANO_REPO = _SOPRANO_SRC.parent.parent
 _SOPRANO_DEFAULT_CACHE = _SOPRANO_REPO / "pipeline_cache"
+_SOPRANO_ENSEMBL_CACHE = _SOPRANO_REPO / "ensembl_downloads"
+_SOPRANO_HOMO_SAPIENS = _SOPRANO_ENSEMBL_CACHE / "homo_sapiens"
 
 # Test dirs
 _SOPRANO_TESTS = _SOPRANO_REPO / "tests"
@@ -49,6 +50,10 @@ def r_scripts(sub_path_item="") -> pathlib.Path:
     def data(sub_path_item="") -> pathlib.Path:
         return _SOPRANO_DATA.joinpath(sub_path_item)
 
+    @staticmethod
+    def ensembl_downloads(sub_path_item="") -> pathlib.Path:
+        return _SOPRANO_ENSEMBL_CACHE.joinpath(sub_path_item)
+
     @staticmethod
     def genomes_homo_sapiens(sub_path_item="") -> pathlib.Path:
         return _SOPRANO_HOMO_SAPIENS.joinpath(sub_path_item)

diff --git a/tests/units/_app_utils_fixtures.py b/tests/units/_app_utils_fixtures.py
@@ -6,6 +6,8 @@
 @pytest.fixture
 def mock_genome_dir():
     assembly, release = "FOO", 999
-    mock_dir = Directories.data() / "homo_sapiens" / f"{release}_{assembly}"
+    mock_dir = (
+        Directories.ensembl_downloads("homo_sapiens") / f"{release}_{assembly}"
+    )
 
     return assembly, release, mock_dir