feat: allow string input

README.md

@@ -24,17 +24,17 @@ python3 -m pip install agct
 Initialize a class instance:
 
 ```python3
-from agct import Converter
-c = Converter("hg38", "hg19")
+from agct import Converter, Genome
+c = Converter(Genome.HG38, Genome.HG19)
 ```
 
-> If a chainfile is unavailable locally, it's downloaded from UCSC and saved using the `wags-tails` package -- see the [configuration instructions](https://github.com/GenomicMedLab/wags-tails?tab=readme-ov-file#configuration) for information on how to designate a non-default storage location.
+> If a chainfile is unavailable locally, it's downloaded from UCSC and saved using the `wags-tails` package -- see the [wags-tails configuration instructions](https://github.com/GenomicMedLab/wags-tails?tab=readme-ov-file#configuration) for information on how to designate a non-default storage location.
 
 Call ``convert_coordinate()``:
 
 ```python3
 c.convert_coordinate("chr7", 140453136, "+")
-# [['chr7', 140152936, '+']]
+# [['chr7', 140152936, <Strand.POSITIVE: '+'>]]
 ```
 
 ## Development

src/agct/converter.py

@@ -38,15 +38,15 @@ class Converter:
 
     def __init__(
         self,
-        from_db: Genome | None = None,
-        to_db: Genome | None = None,
+        from_db: Genome | str | None = None,
+        to_db: Genome | str | None = None,
         chainfile: str | None = None,
     ) -> None:
         """Initialize liftover instance.
 
-        :param from_db: database name, e.g. ``"19"``. Must be different than ``to_db``
+        :param from_db: database name, e.g. ``"hg19"``. 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``
+        :param to_db: database name, e.g. ``"hg38"``. 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
@@ -56,14 +56,27 @@ def __init__(
         :raise _core.ChainfileError: if unable to read chainfile (i.e. it's invalid)
         """
         if not chainfile:
-            if from_db is None and to_db is None:
+            if from_db is None or to_db is None:
                 msg = "Must provide both `from_db` and `to_db`"
                 raise ValueError(msg)
 
             if from_db == to_db:
                 msg = "Liftover must be to/from different sources."
                 raise ValueError(msg)
 
+            if isinstance(from_db, str):
+                try:
+                    from_db = Genome(from_db)
+                except ValueError as e:
+                    msg = f"Unable to coerce from_db value '{from_db}' to a known reference genome: {list(Genome)}"
+                    raise ValueError(msg) from e
+            if isinstance(to_db, str):
+                try:
+                    to_db = Genome(to_db)
+                except ValueError as e:
+                    msg = f"Unable to coerce to_db value '{to_db}' to a known reference genome: {list(Genome)}"
+                    raise ValueError(msg) from e
+
             data_handler = CustomData(
                 f"chainfile_{from_db.value}_to_{to_db.value}",
                 "chain",

tests/test_converter.py

@@ -1,4 +1,6 @@
 """Module for testing Converter initialization"""
+import re
+
 import pytest
 from tests.conftest import DATA_DIR
 
@@ -19,3 +21,11 @@ def test_invalid():
 
     with pytest.raises(ValueError, match="Liftover must be to/from different sources."):
         Converter(Genome.HG19, Genome.HG19)
+
+    with pytest.raises(
+        ValueError,
+        match=re.escape(
+            "Unable to coerce to_db value 'hg18' to a known reference genome: [<Genome.HG38: 'hg38'>, <Genome.HG19: 'hg19'>]"
+        ),
+    ):
+        Converter(Genome.HG19, "hg18")