<!-- This README.md must be keep in sync with doc/source/index.rst manually -->
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[](https://badge.fury.io/py/bed-reader)
[](https://github.com/fastlmm/bed-reader/actions/workflows/ci.yml)
<!-- markdownlint-enable MD041 -->
Read and write the PLINK BED format, simply and efficiently.
*This is the Python README. For Rust, see [README-rust.md](https://crates.io/crates/bed-reader).*
Highlights
====================
* Fast multi-threaded Rust engine.
* Supports all Python indexing methods. Slice data by individuals (samples) and/or SNPs (variants).
* Used by [PySnpTools](https://github.com/fastlmm/PySnpTools), [FaST-LMM](https://github.com/fastlmm/FaST-LMM), and [PyStatGen](https://github.com/pystatgen).
* Supports [PLINK 1.9](https://www.cog-genomics.org/plink2/formats).
* Read data locally or from the cloud, efficiently and directly.
Install
====================
**Full version**: With all optional dependencies:
pip install bed-reader[samples,sparse]
**Minimal version**: Depends only on `numpy`:
pip install bed-reader
Usage
========
Read genomic data from a .bed file.
```python
>>> import numpy as np
>>> from bed_reader import open_bed, sample_file
>>>
>>> file_name = sample_file("small.bed")
>>> bed = open_bed(file_name)
>>> val = bed.read()
>>> print(val)
[[ 1. 0. nan 0.]
[ 2. 0. nan 2.]
[ 0. 1. 2. 0.]]
>>> del bed
```
Read every second individual and SNPs (variants) from 20 to 30.
```python
>>> file_name2 = sample_file("some_missing.bed")
>>> bed2 = open_bed(file_name2)
>>> val2 = bed2.read(index=np.s_[::2,20:30])
>>> print(val2.shape)
(50, 10)
>>> del bed2
```
List the first 5 individual (sample) ids, the
first 5 SNP (variant) ids, and every unique
chromosome. Then, read every genomic value in chromosome 5.
```python
>>> with open_bed(file_name2) as bed3:
... print(bed3.iid[:5])
... print(bed3.sid[:5])
... print(np.unique(bed3.chromosome))
... val3 = bed3.read(index=np.s_[:,bed3.chromosome=='5'])
... print(val3.shape)
['iid_0' 'iid_1' 'iid_2' 'iid_3' 'iid_4']
['sid_0' 'sid_1' 'sid_2' 'sid_3' 'sid_4']
['1' '10' '11' '12' '13' '14' '15' '16' '17' '18' '19' '2' '20' '21' '22'
'3' '4' '5' '6' '7' '8' '9']
(100, 6)
```
From the cloud: open a file and read data for one SNP (variant)
at index position 2.
```python
>>> with open_bed("https://raw.githubusercontent.com/fastlmm/bed-sample-files/main/small.bed") as bed:
... val = bed.read(index=np.s_[:,2], dtype="float64")
... print(val)
[[nan]
[nan]
[ 2.]]
```
Project Links
==============
* [**Documentation**](http://fastlmm.github.io/bed-reader)
* **Questions to**: [fastlmm-dev@python.org](mailto:fastlmm-dev@python.org)
* [**Source code**](https://github.com/fastlmm/bed-reader)
* [**PyPI**](https://pypi.org/project/bed-reader)
* [**Bug reports**](https://github.com/fastlmm/bed-reader/issues)
* [**Mailing list**](https://mail.python.org/mailman3/lists/fastlmm-user.python.org)
* [**Project Website**](https://fastlmm.github.io/)
* [**Change Log**](https://github.com/fastlmm/bed-reader/blob/master/CHANGELOG.md)
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