build: update to latest agct (#442)

The `0.2.0` agct release includes some minor API breaking changes. This
PR resolves them.

It also enables liftover by interval, not just position. I think this
would be good to adopt at some point -- it strikes me as potentially
problematic to just lift over by start and end separately, but
coolseqtool is a little hairy so I left it alone for now.

Author: jsstevenson

pyproject.toml

@@ -26,7 +26,7 @@ license = {file = "LICENSE"}
 dependencies = [
     "asyncpg",
     "boto3",
-    "agct >= 0.1.0-dev1",
+    "agct >= 0.2.0rc1",
     "polars ~= 1.0",
     "biocommons.seqrepo",
     "pydantic >=2.0,<3.0",

src/cool_seq_tool/mappers/liftover.py

@@ -6,7 +6,8 @@
 import logging
 from os import environ
 
-from agct import Converter, Genome
+from agct import Assembly as AgctAssembly
+from agct import Converter
 
 from cool_seq_tool.schemas import Assembly
 from cool_seq_tool.utils import process_chromosome_input
@@ -43,13 +44,13 @@ def __init__(
         """
         self.from_37_to_38 = Converter(
             chainfile=chain_file_37_to_38 or LIFTOVER_CHAIN_37_TO_38,
-            from_db=Genome.HG19,
-            to_db=Genome.HG38,
+            from_assembly=AgctAssembly.HG19,
+            to_assembly=AgctAssembly.HG38,
         )
         self.from_38_to_37 = Converter(
             chainfile=chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37,
-            from_db=Genome.HG38,
-            to_db=Genome.HG19,
+            from_assembly=AgctAssembly.HG38,
+            to_assembly=AgctAssembly.HG19,
         )
 
     def get_liftover(
@@ -77,9 +78,9 @@ def get_liftover(
         """
         chromosome = process_chromosome_input(chromosome, "LiftOver.get_liftover()")
         if liftover_to_assembly == Assembly.GRCH38:
-            liftover = self.from_37_to_38.convert_coordinate(chromosome, pos)
+            liftover = self.from_37_to_38.convert_coordinate(chromosome, pos, pos)
         elif liftover_to_assembly == Assembly.GRCH37:
-            liftover = self.from_38_to_37.convert_coordinate(chromosome, pos)
+            liftover = self.from_38_to_37.convert_coordinate(chromosome, pos, pos)
         else:
             _logger.warning("%s assembly not supported", liftover_to_assembly)
             liftover = None

src/cool_seq_tool/resources/status.py

@@ -114,9 +114,9 @@ async def check_status(
             chain_file_38_to_37=chain_file_38_to_37,
         )
     except (FileNotFoundError, ChainfileError):
-        _logger.exception("agct converter setup failed")
+        _logger.exception("`agct` converter setup failed")
     except Exception as e:
-        _logger.critical("Encountered unexpected error setting up agct: %s", e)
+        _logger.critical("Encountered unexpected error setting up `agct`: %s", e)
     else:
         status["liftover"] = True