toehold requires the following packages to be installed
- python = 3.8
pip install -r requirements.txt
from predict import Infer_ON,Infer_OFF,Infer_ONOFF
seqs = ['AAAATAAGTTAGCTGGATATTGATAAATTTAACAGAGGAGAAAATTTATGAATATCCAG','ATAAACAAAATGGATATTATAGACAAAAAAAACAGAGGAGATTTTTTATGTATAATATC','GATGTTACAAACGATAATATAGACAAAAATAACAGAGGAGAATTTTTATGTATATTATC']
print("ON value:",Infer_ON(seqs))
# ON value: [0.9851788 0.7870039 0.8512967]
print("OFF value:",Infer_OFF(seqs))
# OFF value: [0.71163505 1. 0.9980813 ]
print("ONOFF value:",Infer_ONOFF(seqs))
# ONOFF value: [ 0.12640211 -0.17399795 0.00854342]from optimize import optimize_toehold
seqs = ['AAATTTTATAACCGTTAATATTGATAAAAAAACAGAGGAGATTTTTAATGATATTAACG','ATCTAAGACTAGTGATTTTCTGACTTTCTTAACAGAGGAGAAAGAAAATGAGAAAATCA']
optimized_seqs, new_onoff = optimize_toehold(seqs,num_of_optimization_rounds = 2)
# optimized_seqs ['GGGTTTTACAGCCCTCAATAGATAGATCATAACAGAGGAGAATGATCATGCTATTGAGG','CCCCTCCCCATAAGTTTTGCTACCCTCCCTAACAGAGGAGAAGGGAGATGAGCAAAACT']
# new_onoff [0.9699408, 0.6616005]