typing

Support for type hints.

cbgen.typing.Genotype(probability, phased, …)

Genotype.

cbgen.typing.Partition(offset, variants)

Partition of variants.

cbgen.typing.Variants(id, rsid, chromosome, …)

Variants.

class cbgen.typing.Genotype(probability, phased, ploidy, missing)[source]

Genotype.

>>> import cbgen
>>>
>>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
>>> mf = cbgen.bgen_metafile(cbgen.example.get("haplotypes.bgen.metafile"))
>>> part = mf.read_partition(0)
>>> gt = bgen.read_genotype(part.variants.offset[0])
>>> print(type(gt))
<class 'cbgen.typing.Genotype'>
>>> print(gt.probability)
[[1. 0. 1. 0.]
 [0. 1. 1. 0.]
 [1. 0. 0. 1.]
 [0. 1. 0. 1.]]
>>> print(gt.phased)
True
>>> print(gt.ploidy)
[2 2 2 2]
>>> print(gt.missing)
[False False False False]
>>> mf.close()
>>> bgen.close()
Probability

Probability.

phased

Phasedness.

Type

Any

ploidy

Ploidy.

Type

Any

missing

Missingness.

Type

Any

class cbgen.typing.Partition(offset, variants)[source]

Partition of variants.

>>> import cbgen
>>>
>>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
>>> mf = cbgen.bgen_metafile(cbgen.example.get("haplotypes.bgen.metafile"))
>>> part = mf.read_partition(0)
>>> print(type(part))
<class 'cbgen.typing.Partition'>
>>> print(part.offset)
0
>>> print(type(part.variants))
<class 'cbgen.typing.Variants'>
>>> mf.close()
>>> bgen.close()
offset

Partition offset.

Type

int

variants

Variants.

Type

cbgen.typing.Variants

class cbgen.typing.Variants(id, rsid, chromosome, position, nalleles, allele_ids, offset)[source]

Variants.

>>> import cbgen
>>>
>>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
>>> mf = cbgen.bgen_metafile(cbgen.example.get("haplotypes.bgen.metafile"))
>>> part = mf.read_partition(0)
>>> variants = part.variants
>>> print(type(variants))
<class 'cbgen.typing.Variants'>
>>> print(variants.size)
4
>>> print(variants.id[3])
b'SNP4'
>>> print(variants.rsid[3])
b'RS4'
>>> print(variants.chromosome[3])
b'1'
>>> print(variants.position[3])
4
>>> print(variants.nalleles[3])
2
>>> print(variants.allele_ids[3])
b'A,G'
>>> print(variants.offset[3])
273
>>> mf.close()
>>> bgen.close()
id

Identification.

Type

Any

rsid

Reference SNP cluster ID.

Type

Any

chromosome

Chromosome.

Type

Any

position

Position.

Type

Any

nalleles

Number of alleles per variant.

Type

Any

allele_ids

Allele identifications.

Type

Any

offset

Variant offset.

Type

Any

property size: int

Number of variants.

Return type

int

Returns

Number of variants.