oxbow.from_fastq

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oxbow.from_fastq#

oxbow.from_fastq(source: str | Path | Callable[[], IO[bytes] | str], compression: Literal['infer', 'gzip', None] = 'infer', *, fields: list[str] | None = None, batch_size: int = 131072) → FastqFile#

Create a FASTQ file data source.

Parameters:

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

  • compression (Literal["infer", "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 file extension. For more custom decoding, provide a callable source instead.

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

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

Returns:

A data source object representing the FASTQ file.

Return type:

FastqFile

Notes

Indexed FASTQ files are not supported. Hence, range queries are disallowed and files compressed using either regular GZIP or BGZF are decoded using a standard GZIP decoder.

See also

from_fasta

Create a FASTA file data source.

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