oxbow.core.PyBBIZoomScanner

oxbow.core.PyBBIZoomScanner#

class oxbow.core.PyBBIZoomScanner(src, bbi_type, zoom_level, fields=None)#

A BBI file zoom level scanner.

Can only be initialized from a BigBed or BigWig scanner.

Parameters:

src (str or file-like) – The path to the BBI file or a file-like object.
bbi_type (PyBBIFileType) – The type of BBI file (BigWig or BigBed).
zoom_level (int) – The zoom level resolution in bp.
fields (list[str], optional) – Names of the fields to include in the schema.

Methods

`__init__`()
`field_names`()	Return the names of the reference sequences.
`scan`([columns, batch_size, limit])	Scan batches of records from the zoom level.
`scan_query`(region[, columns, batch_size, limit])	Scan batches of records from a genomic range query.
`schema`()	Return the Arrow schema.

scan(columns=None, batch_size=1024, limit=None)#

Scan batches of records from the zoom level.

Parameters:

columns (list[str], optional) – Names of the columns to project.
batch_size (int, optional [default: 1024]) – The number of records to include in each batch.
limit (int, optional) – The maximum number of records to scan. If None, records are scanned until EOF.

Returns:

An iterator yielding Arrow record batches.

Return type:

arro3 RecordBatchReader (pycapsule)

scan_query(region, columns=None, batch_size=1024, limit=None)#

Scan batches of records from a genomic range query.

Parameters:

region (str) – Genomic region in the format “chr:start-end”.
columns (list[str], optional) – Names of the columns to project.
batch_size (int, optional [default: 1024]) – The number of records to include in each batch.
limit (int, optional) – The maximum number of records to scan. If None, all records intersecting the query range are scanned.

Returns:

An iterator yielding Arrow record batches.

Return type:

arro3 RecordBatchReader (pycapsule)

schema()#

Return the Arrow schema.