feat: allow chainfile argument to be passed to Converter (#26)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "agct"
-version = "0.1.0-dev0"
+version = "0.1.0-dev1"
 authors = [
     {name = "James Stevenson"}
 ]

src/agct/converter.py

@@ -2,7 +2,7 @@
 import logging
 from enum import Enum
 from pathlib import Path
-from typing import Callable, List, Tuple
+from typing import Callable, List, Optional, Tuple
 
 from wags_tails import CustomData
 from wags_tails.utils.downloads import download_http, handle_gzip
@@ -36,35 +36,49 @@ class Converter:
     association.
     """
 
-    def __init__(self, from_db: Genome, to_db: Genome) -> None:
+    def __init__(
+        self,
+        from_db: Optional[Genome] = None,
+        to_db: Optional[Genome] = None,
+        chainfile: Optional[str] = None,
+    ) -> None:
         """Initialize liftover instance.
 
-        :param from_db: database name, e.g. ``"19"``
-        :param to_db: database name, e.g. ``"38"``
+        :param from_db: database name, e.g. ``"19"``. Must be different than ``to_db``
+            If ``chainfile`` is provided, will ignore this argument
+        :param to_db: database name, e.g. ``"38"``. Must be different than ``from_db``
+            If ``chainfile`` is provided, will ignore this argument
+        :param chainfile: Path to chainfile
+            If not provided, must provide both ``from_db`` and ``to_db`` so that
+            ``wags-tails`` can download the corresponding chainfile
+        :raise ValueError: if required arguments are not passed or are invalid
         :raise FileNotFoundError: if unable to open corresponding chainfile
         :raise _core.ChainfileError: if unable to read chainfile (i.e. it's invalid)
         """
-        if from_db == to_db:
-            raise ValueError("Liftover must be to/from different sources.")
-        if not isinstance(from_db, Genome):
-            from_db = Genome(from_db)
-        if not isinstance(to_db, Genome):
-            to_db = Genome(to_db)
-        data_handler = CustomData(
-            f"chainfile_{from_db.value}_to_{to_db.value}",
-            "chain",
-            lambda: "",
-            self._download_function_builder(from_db, to_db),
-            data_dir=get_data_dir() / "ucsc-chainfile",
-        )
-        file, _ = data_handler.get_latest()
+        if not chainfile:
+            if from_db is None and to_db is None:
+                raise ValueError("Must provide both `from_db` and `to_db`")
+
+            if from_db == to_db:
+                raise ValueError("Liftover must be to/from different sources.")
+
+            data_handler = CustomData(
+                f"chainfile_{from_db.value}_to_{to_db.value}",
+                "chain",
+                lambda: "",
+                self._download_function_builder(from_db, to_db),
+                data_dir=get_data_dir() / "ucsc-chainfile",
+            )
+            file, _ = data_handler.get_latest()
+            chainfile = str(file.absolute())
+
         try:
-            self._converter = _core.Converter(str(file.absolute()))
+            self._converter = _core.Converter(chainfile)
         except FileNotFoundError as e:
-            _logger.error("Unable to open chainfile located at %s", file.absolute())
+            _logger.error("Unable to open chainfile located at %s", chainfile)
             raise e
         except _core.ChainfileError as e:
-            _logger.error("Error reading chainfile located at %s", file.absolute())
+            _logger.error("Error reading chainfile located at %s", chainfile)
             raise e
 
     @staticmethod

tests/test_converter.py

@@ -0,0 +1,21 @@
+"""Module for testing Converter initialization"""
+import pytest
+from tests.conftest import DATA_DIR
+
+from agct import Converter, Genome
+
+
+def test_valid():
+    """Test valid initialization"""
+    assert Converter(
+        chainfile=str(DATA_DIR / "ucsc-chainfile" / "chainfile_hg19_to_hg38_.chain")
+    )
+
+
+def test_invalid():
+    """Test invalid initialization"""
+    with pytest.raises(ValueError, match="Must provide both `from_db` and `to_db`"):
+        Converter()
+
+    with pytest.raises(ValueError, match="Liftover must be to/from different sources."):
+        Converter(Genome.HG19, Genome.HG19)