oxbow.from_bed

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oxbow.from_bed#

oxbow.from_bed(source: str | pathlib.Path | Callable[[], IO[bytes] | str], bed_schema: BedSchemaLike = 'bed3+', compression: Literal['infer', 'bgzf', 'gzip', None] = 'infer', *, fields: Literal['*'] | list[str] | None = '*', coords: Literal['01', '11'] = '01', regions: str | list[str] | None = None, index: str | pathlib.Path | Callable[[], IO[bytes] | str] | None = None, batch_size: int = 131072) → BedFile#

Create a BED file data source.

Parameters:

  • source (str, pathlib.Path, or Callable) – The URI or path to the BED file, or a callable that opens the file as a file-like object.

  • bed_schema (str or tuple[str, list | dict], optional) – Schema for interpreting the BED file. Can be a specifier string (e.g., “bed6”, “bed3+”, “bedgraph”) or a tuple of (base_specifier, custom_defs) where custom_defs is a list of (name, type) tuples or a dict mapping field names to type strings. The default is “bed3+”, which includes the first three standard fields and lumps any additional data into a “rest” column.

  • compression (Literal["infer", "bgzf", "gzip", None], default: "infer") – Compression of the source bytestream. If “infer” and source is a URI or path, the file’s compression is guessed based on the extension, where “.gz” or “.bgz” is interpreted as BGZF. Pass “gzip” to decode regular GZIP. If None, the source bytestream is assumed to be uncompressed. For more customized decoding, provide a callable source instead.

  • fields (list[str], optional) – Specific fields to project as columns. By default, all available fields are included.

  • regions (str | list[str], optional) – One or more genomic regions to query. Only applicable if an associated index file is available.

  • index (str, pathlib.Path, or Callable, optional) – An optional index file associated with the GTF file. If source is a URI or path, is BGZF-compressed, and the index file shares the same name with a “.tbi” or “.csi” extension, the index file is automatically detected.

  • batch_size (int, optional [default: 131072]) – The number of records to read in each batch.

Returns:

A data source object representing the BED file.

Return type:

BedFile

See also

from_gtf

Create a GTF file data source.

from_gff

Create a GFF file data source.

from_bigbed

Create a BigBed file data source.

from_bigwig

Create a BigWig file data source.

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