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update docs
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korikuzma committed Nov 7, 2023
1 parent 9985b40 commit ac8117d
Showing 1 changed file with 8 additions and 2 deletions.
10 changes: 8 additions & 2 deletions cool_seq_tool/data_sources/feature_overlap.py
Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,10 @@ def get_grch38_mane_gene_cds_overlap(
identifier: Optional[str] = None,
residue_mode: ResidueMode = ResidueMode.RESIDUE,
) -> Optional[Dict[str, CdsOverlap]]:
"""Given GRCh38 genomic data, find the overlapping MANE features (gene and cds)
"""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
pair overlap will be returned.
:param start: GRCh38 start position
:param end: GRCh38 end position
Expand All @@ -138,7 +141,10 @@ def get_grch38_mane_gene_cds_overlap(
:param residue_mode: Residue mode for `start` and `end`
:raise FeatureOverlapError: If missing required fields or unable to find
associated ga4gh identifier
:return: MANE feature (gene/cds) overlap data represented as a dict
:return: MANE feature (gene/cds) overlap data represented as a dict. The
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
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