| Name | plink-bed-reader JSON |
| Version |
1.0.2
JSON |
| download |
| home_page | None |
| Summary | Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in pure Python. |
| upload_time | 2025-02-21 12:29:28 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.6 |
| license | MIT |
| keywords |
bed
plink
genetics
bioinformatics
variant
indel
snv
genotype
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# PLINK BED reader<!-- omit in toc -->
**Lightweight and memory efficient reader for PLINK BED files**. It supports both SNP-major and individual-major formats. Written in Python 3. Check the [available documentation](https://computational-genomics-bsc.github.io/plink-bed-reader/) for more information.
## Table of contents<!-- omit in toc -->
- [Getting started](#getting-started)
- [Installation](#installation)
- [Usage](#usage)
- [Dependencies](#dependencies)
## Getting started
### Installation
`plink-bed-reader` is available on PyPI and can be installed using `pip`:
```bash
pip install plink-bed-reader
```
## Usage
```python
# Import the package
from plink_bed_reader import PLINKBEDReader, BEDMode
# Load the PLINK BED file (we include the mode for sanity check, but it is optional)
bed = PLINKBEDReader('./input_test_data/test.bed', mode=BEDMode.SNP_MAJOR)
# Print the number of SNPs and samples
print('Number of SNPs:', bed.snp_count)
print('Number of samples:', bed.sample_count)
# Print the first SNP
first_snp = bed[0]
print('First SNP:', first_snp, first_snp.dtype)
# Print the first 3 SNPs
print('First 3 SNPs:', bed[:3])
```
## Dependencies
The dependencies are covered by their own respective licenses as follows:
* [Python/NumPy package](https://numpy.org/)
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"description": "# PLINK BED reader<!-- omit in toc -->\n**Lightweight and memory efficient reader for PLINK BED files**. It supports both SNP-major and individual-major formats. Written in Python 3. Check the [available documentation](https://computational-genomics-bsc.github.io/plink-bed-reader/) for more information.\n\n## Table of contents<!-- omit in toc -->\n- [Getting started](#getting-started)\n - [Installation](#installation)\n- [Usage](#usage)\n- [Dependencies](#dependencies)\n\n\n## Getting started\n### Installation\n`plink-bed-reader` is available on PyPI and can be installed using `pip`:\n```bash\npip install plink-bed-reader\n```\n\n## Usage\n```python\n# Import the package\nfrom plink_bed_reader import PLINKBEDReader, BEDMode\n\n# Load the PLINK BED file (we include the mode for sanity check, but it is optional)\nbed = PLINKBEDReader('./input_test_data/test.bed', mode=BEDMode.SNP_MAJOR)\n\n# Print the number of SNPs and samples\nprint('Number of SNPs:', bed.snp_count)\nprint('Number of samples:', bed.sample_count)\n# Print the first SNP\nfirst_snp = bed[0]\nprint('First SNP:', first_snp, first_snp.dtype)\n# Print the first 3 SNPs\nprint('First 3 SNPs:', bed[:3])\n```\n\n## Dependencies\n\nThe dependencies are covered by their own respective licenses as follows:\n\n* [Python/NumPy package](https://numpy.org/)\n",
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