diff options
Diffstat (limited to 'gn3/api/search.py')
| -rw-r--r-- | gn3/api/search.py | 14 |
1 files changed, 10 insertions, 4 deletions
diff --git a/gn3/api/search.py b/gn3/api/search.py index f696428..6aed2ad 100644 --- a/gn3/api/search.py +++ b/gn3/api/search.py @@ -6,7 +6,7 @@ import gzip import json from functools import partial, reduce from pathlib import Path -from typing import Callable +from typing import Union, Callable import urllib.parse from flask import abort, Blueprint, current_app, jsonify, request @@ -65,7 +65,10 @@ def field_processor_or(*field_processors: FieldProcessorFunction) -> FieldProces for field_processor in field_processors])) -def liftover(chain_file: Path, position: ChromosomalPosition) -> Maybe[ChromosomalPosition]: +def liftover( + chain_file: Union[str, Path], + position: ChromosomalPosition +) -> Maybe[ChromosomalPosition]: """Liftover chromosomal position using chain file.""" # The chain file format is described at # https://genome.ucsc.edu/goldenPath/help/chain.html @@ -91,7 +94,10 @@ def liftover(chain_file: Path, position: ChromosomalPosition) -> Maybe[Chromosom return Nothing -def liftover_interval(chain_file: str, interval: ChromosomalInterval) -> ChromosomalInterval: +def liftover_interval( + chain_file: Union[str, Path], + interval: ChromosomalInterval +) -> ChromosomalInterval: """ Liftover interval using chain file. @@ -258,7 +264,7 @@ def parse_query(synteny_files_directory: Path, query: str): xapian.Query(species_prefix + lifted_species), chromosome_prefix, range_prefixes.index("position"), - partial(liftover_interval, + partial(liftover_interval,# type: ignore[arg-type] synteny_files_directory / chain_file))) queryparser.add_boolean_prefix( shorthand, |