oxbow.core.PyBigWigScanner

class oxbow.core.PyBigWigScanner(src)

A BigWig file scanner.

Parameters:

src (str or file-like) – The path to the BigWig file or a file-like object.

__init__()

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)	Return a scanner for a specific zoom level.
scan([fields, batch_size, limit])	Scan batches of records from the file.
scan_query(region[, fields, batch_size, limit])	Scan batches of records from a genomic range query.
schema([fields])	Return the Arrow schema.
zoom_levels()	Return the zoom/reduction level resolutions.

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)

Return a scanner for a specific zoom level.

Parameters:

zoom_level (int) – The resolution (in bp) of the zoom level to scan.

Returns:

A scanner for the specified zoom level.

Return type:

PyBBIZoomScanner

scan(fields=None, batch_size=1024, limit=None)

Scan batches of records from the file.

Parameters:

• fields (list[str], optional) – Names of the fixed fields 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, fields=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”.

• fields (list[str], optional) – Names of the fixed fields 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(fields=None)

Return the Arrow schema.

Parameters:

fields (list[str], optional) – Names of the fields to project.

Return type:

arro3 Schema (pycapsule)

zoom_levels()

Return the zoom/reduction level resolutions.