https://github.com/KennthShang/PhaGCN2.0
安装
mamba create -n phagcn2 python=3.9 numpy pytorch networkx pandas mcl diamond biopython scipy
conda activate phagcn2
git clone https://github.com/KennthShang/PhaGCN2.0
cd database
tar -zxvf ALL_protein.tar.gz
cd ..
把PhaGCN2.0/data.py的
from scipy.sparse.linalg.eigen.arpack import eigsh
改成from scipy.sparse.linalg import eigsh
eturn np.array(mask, dtype=np.bool)
改为eturn np.array(mask, dtype=bool)
PhaGCN2.0/run_GCN.py
也这么改
使用
python run_Speed_up.py --contigs contigs.fa --len 8000
