Ensure that your compute environment allows you to run JAX code. (A modern Linux or macOS with a GLIBC>=2.23 is probably necessary.)
Then, install from PyPI:
pip install jax-unirep
On the roadmap is support for installation from PyPI and conda-forge.
The core activity with using UniRep
is to produce fixed-length representations of protein sequences.
This is done by using the
You can "rep" a single sequence:
from jax_unirep import get_reps sequence = "ASDFGHJKL" # h_avg is the canonical "reps" h_avg, h_final, c_final = get_reps(sequence)
Or you can "rep" a bunch of sequences together:
from jax_unirep import get_reps sequences = ["ASDF", "YJKAL", "QQLAMEHALQP"] # h_avg is the canonical "reps" h_avg, h_final, c_final= get_reps(sequences) # each of the arrays will be of shape (len(sequences), 1900), # with the correct order of sequences preserved
Canonically, you would use
h_avg as the "reps".