sdfljk

Author: jsstevenson

src/agct/__init__.py

@@ -1,6 +1,12 @@
 """Provide fast liftover in Python via the ``chainfile`` crate."""
 
 from agct.assembly_registry import Assembly, get_assembly_from_refget_id
-from agct.converter import Converter, Strand
+from agct.converter import Converter, LiftoverResult, Strand
 
-__all__ = ["Assembly", "Converter", "Strand", "get_assembly_from_refget_id"]
+__all__ = [
+    "Assembly",
+    "Converter",
+    "LiftoverResult",
+    "Strand",
+    "get_assembly_from_refget_id",
+]

src/agct/converter.py

@@ -4,6 +4,7 @@
 from collections.abc import Callable
 from enum import Enum
 from pathlib import Path
+from typing import NamedTuple
 
 from wags_tails import CustomData
 from wags_tails.utils.downloads import download_http, handle_gzip
@@ -22,6 +23,14 @@ class Strand(str, Enum):
     NEGATIVE = "-"
 
 
+class LiftoverResult(NamedTuple):
+    """Declare structure of liftover response"""
+
+    chrom: str
+    position: int
+    strand: Strand
+
+
 class Converter:
     """Chainfile-based liftover provider for a single sequence to sequence
     association.
@@ -113,7 +122,7 @@ def _download_data(version: str, file: Path) -> None:  # noqa: ARG001
 
     def convert_coordinate(
         self, chrom: str, pos: int, strand: Strand = Strand.POSITIVE
-    ) -> list[tuple[str, int, Strand]]:
+    ) -> list[LiftoverResult]:
         """Perform liftover for given params
 
         The ``Strand`` enum provides constraints for legal strand values:
@@ -144,7 +153,7 @@ def convert_coordinate(
                 strand,
             )
             results = []
-        formatted_results: list[tuple[str, int, Strand]] = []
+        formatted_results: list[LiftoverResult] = []
         for result in results:
             try:
                 pos = int(result[1])
@@ -156,5 +165,5 @@ def convert_coordinate(
             except ValueError:
                 _logger.exception("Got invalid Strand value in %s", result)
                 continue
-            formatted_results.append((result[0], pos, strand))
+            formatted_results.append(LiftoverResult(result[0], pos, strand))
         return formatted_results

tests/test_liftover.py

@@ -1,6 +1,6 @@
 """Run liftover tests."""
 
-from agct import Assembly, Converter, Strand
+from agct import Assembly, Converter, LiftoverResult, Strand
 
 
 def test_hg19_to_hg38():
@@ -9,23 +9,23 @@ def test_hg19_to_hg38():
 
     result = converter.convert_coordinate("chr7", 140439611)
     assert len(result) == 1
-    assert result[0] == ("chr7", 140739811, Strand.POSITIVE)
+    assert result[0] == LiftoverResult("chr7", 140739811, Strand.POSITIVE)
 
     result = converter.convert_coordinate("chr7", 140439746)
     assert len(result) == 1
-    assert result[0] == ("chr7", 140739946, Strand.POSITIVE)
+    assert result[0] == LiftoverResult("chr7", 140739946, Strand.POSITIVE)
 
     result = converter.convert_coordinate("chr7", 140439703)
     assert len(result) == 1
-    assert result[0] == ("chr7", 140739903, Strand.POSITIVE)
+    assert result[0] == LiftoverResult("chr7", 140739903, Strand.POSITIVE)
 
     result = converter.convert_coordinate("chr7", 140453136)
     assert len(result) == 1
-    assert result[0] == ("chr7", 140753336, Strand.POSITIVE)
+    assert result[0] == LiftoverResult("chr7", 140753336, Strand.POSITIVE)
 
     result = converter.convert_coordinate("chr1", 206072707)
     assert len(result) == 1
-    assert result[0] == ("chr1", 206268644, Strand.NEGATIVE)
+    assert result[0] == LiftoverResult("chr1", 206268644, Strand.NEGATIVE)
 
     # coordinate exceeds bounds
     result = converter.convert_coordinate("chr7", 14040053136)
@@ -38,12 +38,12 @@ def test_hg38_to_hg19():
 
     result = converter.convert_coordinate("chr7", 140739811)
     assert len(result) == 1
-    assert result[0] == ("chr7", 140439611, Strand.POSITIVE)
+    assert result[0] == LiftoverResult("chr7", 140439611, Strand.POSITIVE)
 
     result = converter.convert_coordinate("chr7", 140759820)
     assert len(result) == 1
-    assert result[0] == ("chr7", 140459620, Strand.POSITIVE)
+    assert result[0] == LiftoverResult("chr7", 140459620, Strand.POSITIVE)
 
     result = converter.convert_coordinate("chr7", 60878240)
     assert len(result) == 1
-    assert result[0] == ("chr7", 61646115, Strand.POSITIVE)
+    assert result[0] == LiftoverResult("chr7", 61646115, Strand.POSITIVE)