ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing

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 git@github.com: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

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