diff --git a/cool_seq_tool/data_sources/feature_overlap.py b/cool_seq_tool/data_sources/feature_overlap.py index eb50ce60..f7d5cdce 100644 --- a/cool_seq_tool/data_sources/feature_overlap.py +++ b/cool_seq_tool/data_sources/feature_overlap.py @@ -1,7 +1,7 @@ """Module for getting feature (gene/exon) overlap""" import re from pathlib import Path -from typing import Dict, Optional +from typing import Dict, Optional, List import pandas as pd from ga4gh.core import ga4gh_identify @@ -124,7 +124,7 @@ def get_grch38_mane_gene_cds_overlap( chromosome: Optional[str] = None, identifier: Optional[str] = None, residue_mode: ResidueMode = ResidueMode.RESIDUE, - ) -> Optional[Dict[str, CdsOverlap]]: + ) -> Optional[Dict[str, List[CdsOverlap]]]: """Given GRCh38 genomic data, find the overlapping MANE features (gene and cds). The genomic data is specified as a sequence location by `chromosome`, `start`, `end`. All CDS regions with which the input sequence location has nonzero base @@ -145,12 +145,6 @@ def get_grch38_mane_gene_cds_overlap( dictionary will be keyed by genes which overlap the input sequence location. Each gene contains a list of the overlapping CDS regions with the beginning and end of the input sequence location's overlap with each - { - gene: { - 'cds': VRS Sequence Location - 'overlap': VRS Sequence Location - } - } """ ga4gh_seq_id = None if chromosome: diff --git a/cool_seq_tool/version.py b/cool_seq_tool/version.py index 659f176c..becaf0f3 100644 --- a/cool_seq_tool/version.py +++ b/cool_seq_tool/version.py @@ -1 +1 @@ -__version__ = "0.1.14-dev2" +__version__ = "0.1.14-dev3"