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build: update to latest agct #442

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Merged
jsstevenson merged 2 commits into from
Oct 29, 2025
Merged

build: update to latest agct #442

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cc0236b
build: update to latest agct
jsstevenson Oct 29, 2025
36a7b06
lil commit
jsstevenson Oct 29, 2025
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
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15 changes: 8 additions & 7 deletions src/cool_seq_tool/mappers/liftover.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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
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4 changes: 2 additions & 2 deletions src/cool_seq_tool/resources/status.py
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Expand Up @@ -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

Expand Down