This repository contains inference code for A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing (ContraNovo)
-
Get resource and create the conda environment.
git clone [email protected]:BEAM-Labs/ContraNovo.git cd ContraNovo conda env create -f platform_independent_environment.yml conda activate ContraNovo -
Download ContraNovo checkpoint and Bacillus.10k.mgf from google drive.
ContraNovo.ckpt ：https://drive.google.com/file/d/1knNUqSwPf98j388Ds2E6bG8tAXx8voWR/view?usp=drive_link
Bacillus.10k.mgf : https://drive.google.com/file/d/1HqfCETZLV9ZB-byU0pqNNRXbaPbTAceT/view?usp=drive_link
-
Run ContraNovo test on bacillus.10k.mgf
python -m ContraNovo.ContraNovo --mode=vectors --peak_path=./ContraNovo/bacillus.10k.mgf --model=./ContraNovo/ContraNovo.ckpt