brisket 0.1.1

Fast Cython-powered one-hot encoding for DNA sequences

brisket

Fast cython powered 1 hot encoding for DNA sequences

Installation

$ pip install brisket

Usage

import numpy as np
from brisket import encode_seq

# Encode a DNA sequence to one-hot format
dna_sequence = "ATCG"
encoded = encode_seq(dna_sequence)

print(encoded)
# Output: 2D numpy array with shape (seq_length, 4)
# [[1 0 0 0]  # A
#  [0 0 0 1]  # T  
#  [0 1 0 0]  # C
#  [0 0 1 0]] # G

# The encoding maps: A=column 0, C=column 1, G=column 2, T=column 3
# Each row represents one nucleotide position
# Each column represents one of the four DNA bases (A, C, G, T)

# Invalid characters (not A, T, C, G) result in all-zero rows
encoded_with_n = encode_seq("ATCGN")  # Last row will be [0 0 0 0]

Contributing

Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

brisket was created by Natalie Gill and Sean Whalen. It is licensed under the terms of the MIT license.

Credits

brisket was created with cookiecutter and the py-pkgs-cookiecutter template.