Data Lake¶

AIDO Datalake endpoints for querying biological reference data (AIDO_DATALAKE_URL).

Gene¶

genbio.data.aido_datalake_apis.gene_histone ¶

gene_histone(cell_type: str, mark: str, chrom: str, start: int, end: int) -> list[dict[str, Any]]

Return raw bigWig signal intervals for a histone mark over a genomic region.

Queries the AIDO Datalake for histone ChIP-seq signal stored as bigWig files. Accepts explicit chromosomal coordinates only. To query by gene symbol, first resolve coordinates via gene_interval (GET /data/gene/interval).

Parameters:

Name	Type	Description	Default
`cell_type`	`str`	The cell type identifier (e.g. `"K562"`).	required
`mark`	`str`	The histone mark to query (e.g. `"H3K27ac"`, `"H3K4me3"`).	required
`chrom`	`str`	Chromosome name (e.g. `"chr1"`). Both `"chr1"` and `"1"` forms are accepted; the server normalises the name against the bigWig header.	required
`start`	`int`	0-based genomic start coordinate (inclusive).	required
`end`	`int`	0-based genomic end coordinate (exclusive).	required

Returns:

Type	Description
`list[dict[str, Any]]`	A list of interval dicts, each with the following keys:
`list[dict[str, Any]]`	`"start"` (int): Genomic start coordinate of the interval.
`list[dict[str, Any]]`	`"end"` (int): Genomic end coordinate of the interval.
`list[dict[str, Any]]`	`"value"` (float): Raw bigWig signal value for the interval.

Raises:

Type	Description
`HTTPError`	On 400 (invalid mark or chromosome), 404 (cell type / mark not found), or 503 (bigWig file missing on the server), with the response body included in the error message.

Example::

intervals = gene_histone(
    cell_type="K562",
    mark="H3K27ac",
    chrom="chr1",
    start=1_000_000,
    end=1_010_000,
)
for iv in intervals:
    print(iv["start"], iv["end"], iv["value"])