bgen-reader 0.1.16

Bgen file format reader.

# Bgen-reader

[](https://travis-ci.org/limix/bgen-reader-py)
[](https://pypi.python.org/pypi/bgen-reader/)
[](https://pypi.python.org/pypi/bgen-reader/)
[](https://pypi.python.org/pypi/bgen-reader/)
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A [BGEN file format](http://www.well.ox.ac.uk/~gav/bgen_format/) reader.

BGEN is a file format for storing large genetic datasets. It supports both unphased genotypes and phased haplotype data with variable ploidy and number of alleles. It was designed to provides a compact data representation without sacrificing variant access performance.

This Python package is a wrapper around the [bgen library](https://github.com/limix/bgen),
a low-memory footprint reader that efficiently reads BGEN files.
It fully supports all the BGEN format specifications: 1.1, 1.2, and 1.3;
as well as their optional compressed formats.

## Install

The recommended way of installing it is via
[conda](http://conda.pydata.org/docs/index.html)

```bash
conda install -c conda-forge bgen-reader
```

An alternative way would be via pip

```bash
pip install bgen-reader
```

In this case, you need to make sure you have both
[Zstandard](https://github.com/facebook/zstd) and [bgen](https://github.com/limix/bgen)
libraries properly installed.

## Usage

It is as simple as

```python
# example.py file
from bgen_reader import read_bgen

bgen = read_bgen("example.bgen", verbose=False)

print(bgen['variants'].head())
print(bgen['samples'].head())
print(len(bgen['genotype']))
print(bgen['genotype'][0].compute())
```

The output should something similar to

```
chrom id nalleles pos rsid
0 01 SNPID_2 2 2000 RSID_2
1 01 SNPID_3 2 3000 RSID_3
2 01 SNPID_4 2 4000 RSID_4
3 01 SNPID_5 2 5000 RSID_5
4 01 SNPID_6 2 6000 RSID_6
id
0 sample_001
1 sample_002
2 sample_003
3 sample_004
4 sample_005
199
[[ nan nan nan]
[ 0.02780236 0.00863674 0.9635609 ]
[ 0.01736504 0.04968414 0.93295083]
...,
[ 0.01419069 0.02810669 0.95770262]
[ 0.91949463 0.05206298 0.02844239]
[ 0.00244141 0.98410029 0.0134583 ]]
```

## Problems

If you encounter any issue, please, [submit it](https://github.com/limix/bgen-reader-py/issues).

## Authors

* **Danilo Horta** - [https://github.com/horta](https://github.com/horta)

## License

This project is licensed under the MIT License - see the
[LICENSE](LICENSE) file for details