华大空间转录组Stereo-seq数据转化为seurat对象

基于python的stereopy库将gem文件批量转化为h5ad(seurat可识别)文件 

import numpy
import numba
import warnings
warnings.filterwarnings('ignore')
import stereo as st
import os 

def gem_to_h5ad(data_path,file,bins): 
    data = st.io.read_gem(file_path=str(data_path+file),sep='\t',bin_type='bins',bin_size=bins,is_sparse=True)
    #read the gem file as data
    #导出的h5ad文件
    data.tl.raw_checkpoint()
    st.io.stereo_to_anndata(data,flavor='seurat',output=str(data_path+str.split(file,'.')[2]+'.h5ad'))

gz_files = [file for file in os.listdir('/home/xintong/BGI_STO_koutu/5DAP') if file.endswith('.gz')]
data_path='/home/xintong/BGI_STO_koutu/5DAP/'
bins=50
for file in gz_files:
    gem_to_h5ad(data_path,file,bins)

使用R包SeuratDisk 将h5ad文件批量转化为Seurat函数能识别的h5seurat文件 

library(Seurat,lib.loc='/home/xintong/anaconda3/envs/r40/lib/R/library/',verbose=F)
library(SeuratDisk,lib.loc='/home/xintong/anaconda3/envs/r40/