plink-bed-reader 1.0.1
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Description:
plinkbedreader 1.0.1
PLINK BED reader
Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in pure Python. Check the available documentation for more information.
Table of contents
Getting started
Installation
Usage
Dependencies
Getting started
Installation
plink-bed-reader is available on PyPI and can be installed using pip:
pip install plink-bed-reader
Usage
# 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
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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