From ef33d8718e694f30004f2b81f7ba6fd988dbc794 Mon Sep 17 00:00:00 2001 From: Isaac Virshup Date: Wed, 3 Apr 2024 23:42:28 +1100 Subject: [PATCH] Fix import (#60) --- src/genomic_features/ensembl/ensembldb.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/genomic_features/ensembl/ensembldb.py b/src/genomic_features/ensembl/ensembldb.py index a731470..1b148fe 100644 --- a/src/genomic_features/ensembl/ensembldb.py +++ b/src/genomic_features/ensembl/ensembldb.py @@ -14,8 +14,8 @@ from requests.exceptions import HTTPError from genomic_features import filters -from genomic_features._core import filters as _filters from genomic_features._core.cache import retrieve_annotation +from genomic_features._core.filters import AbstractFilterExpr PKG_CACHE_DIR = "genomic-features" @@ -145,7 +145,7 @@ def __repr__(self) -> str: def genes( self, cols: list[str] | None = None, - filter: _filters.AbstractFilterExpr = filters.EmptyFilter(), + filter: AbstractFilterExpr = filters.EmptyFilter(), join_type: Literal["inner", "left"] = "inner", ) -> DataFrame: """Get gene annotations. @@ -180,7 +180,7 @@ def genes( def transcripts( self, cols: list[str] | None = None, - filter: _filters.AbstractFilterExpr = filters.EmptyFilter(), + filter: AbstractFilterExpr = filters.EmptyFilter(), join_type: Literal["inner", "left"] = "inner", ) -> DataFrame: """Get transcript annotations. @@ -218,7 +218,7 @@ def transcripts( def exons( self, cols: list[str] | None = None, - filter: _filters.AbstractFilterExpr = filters.EmptyFilter(), + filter: AbstractFilterExpr = filters.EmptyFilter(), join_type: Literal["inner", "left"] = "inner", ) -> DataFrame: """Get exons table. @@ -273,7 +273,7 @@ def _build_query( self, table: Literal["gene", "tx", "exon"], cols: list[str], - filter: _filters.AbstractFilterExpr, + filter: AbstractFilterExpr, join_type: Literal["inner", "left"] = "inner", ) -> IbisTable: """Build a query for the genomic features table."""