Read

bgen_reader.read_bgen(filepath: Union[str, pathlib.Path], metafile_filepath: Optional[Union[str, pathlib.Path]] = None, samples_filepath: Optional[Union[str, pathlib.Path]] = None, verbose: bool = True)[source]

Read a given BGEN file.

Parameters

  • filepath – Bgen file path.

  • metafile_filepath – File path to the corresponding metafile. A metafile can be created by calling bgen_reader.create_metafile(). If None, a metafile will be automatically created. Defaults to None.

  • samples_filepath – Path to a sample format file or None to read samples from the bgen file itself. Defaults to None.

  • verbose – True to show progress; False otherwise. Defaults to True.

Returns

  • variants (dask.dataFrame.DataFrame) – Variant position, chromosomes, rsids, etc.

  • samples (pandas.Series) – Sample identifications.

  • genotype (list) – List of genotypes.

Examples

>>> from bgen_reader import example_filepath, read_bgen
>>>
>>> bgen = read_bgen(example_filepath("haplotypes.bgen"), verbose=False)
>>> variants = bgen["variants"]
>>> samples = bgen["samples"]
>>>
>>> v = variants.loc[0].compute()
>>> g = bgen["genotype"][0].compute()
>>> print(v)
     id rsid chrom  pos  nalleles allele_ids  vaddr
0  SNP1  RS1     1    1         2        A,G    102
>>> print(samples)
0    sample_0
1    sample_1
2    sample_2
3    sample_3
Name: id, dtype: object
>>> print(g["probs"][0])
[1. 0. 1. 0.]