update agct version

GenomicMedLab · Feb 2, 2024 · ca43d31 · ca43d31
1 parent 0dd2c86
commit ca43d31
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -29,7 +29,7 @@ dependencies = [
     "asyncpg",
     "aiofiles",
     "boto3",
-    "agct",
+    "agct >= 0.1.0-dev1",
     "polars",
     "hgvs",
     "biocommons.seqrepo",

diff --git a/src/cool_seq_tool/sources/uta_database.py b/src/cool_seq_tool/sources/uta_database.py
@@ -10,7 +10,7 @@
 import asyncpg
 import boto3
 import polars as pl
-from agct import Converter
+from agct import Converter, Genome
 from asyncpg.exceptions import InterfaceError, InvalidAuthorizationSpecificationError
 from botocore.exceptions import ClientError
 
@@ -71,15 +71,15 @@ def __init__(
 
         chain_file_37_to_38 = chain_file_37_to_38 or LIFTOVER_CHAIN_37_TO_38
         if chain_file_37_to_38:
-            self.liftover_37_to_38 = Converter(chain_file_37_to_38)
+            self.liftover_37_to_38 = Converter(chainfile=chain_file_37_to_38)
         else:
-            self.liftover_37_to_38 = Converter("hg19", "hg38")
+            self.liftover_37_to_38 = Converter(from_db=Genome.HG19, to_db=Genome.HG38)
 
         chain_file_38_to_37 = chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37
         if chain_file_38_to_37:
-            self.liftover_38_to_37 = Converter(chain_file_38_to_37)
+            self.liftover_38_to_37 = Converter(chainfile=chain_file_38_to_37)
         else:
-            self.liftover_38_to_37 = Converter("hg38", "hg19")
+            self.liftover_38_to_37 = Converter(from_db=Genome.HG38, to_db=Genome.HG19)
 
     def _get_conn_args(self) -> Dict:
         """Return connection arguments.