oxbow.core.PyBigWigScanner

oxbow.core.PyBigWigScanner#

class oxbow.core.PyBigWigScanner(src, fields=None)#

A BigWig file scanner.

Parameters:

src (str or file-like) – The path to the BigWig file or a file-like object.
fields (list[str], optional) – Names of the fields to include in the schema.

Methods

`__init__`()
`chrom_names`()	Return the names of the reference sequences.
`chrom_sizes`()	Return the names of the reference sequences and their lengths in bp.
`field_names`()	Return the names of the fields.
`get_zoom`(zoom_level[, fields])	Return a scanner for a specific zoom level.
`scan`([columns, batch_size, limit])	Scan batches of records from the file.
`scan_query`(region[, columns, batch_size, limit])	Scan batches of records from a genomic range query.
`schema`()	Return the Arrow schema.
`zoom_levels`()	Return the zoom/reduction level resolutions.

chrom_sizes()#: Return the names of the reference sequences and their lengths in bp.

get_zoom(zoom_level, fields=None)#

Return a scanner for a specific zoom level.

Parameters:

zoom_level (int) – The resolution (in bp) of the zoom level to scan.
fields (list[str], optional) – Names of the fields to include in the zoom schema.

Returns:

A scanner for the specified zoom level.

Return type:

PyBBIZoomScanner

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

Scan batches of records from the file.

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.