https://github.com/KennthShang/PhaGCN2.0
安装
mamba create -n phagcn2 python=3.9 numpy pytorch networkx=2.5 pandas mcl=14.137 diamond=0.9.14 biopython=1.78 scipy=1.5.2
conda activate phagcn2
git clone https://github.com/KennthShang/PhaGCN2.0cd 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 eigsheturn 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
