华大空间转录组Stereo-seq数据转化为seurat对象

 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)
    
    
    
    
    python
    
    
![](https://ad.itadn.com/c/weblog/blog-img/images/2025-08-16/95cqWet2OvXusnfK3JydRzNI7m4x.png)

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

    
 library(SeuratDisk,lib.loc='/home/xintong/anaconda3/envs/r40/lib/R/library/',verbose=F)
    
  
    
 setwd('/home/xintong/BGI_STO_koutu/5DAP/')
    
 files = list.files('./',pattern = '.h5ad$',full.names = F, recursive = FALSE, include.dirs = FALSE)
    
 files
    
  
    
 for (file in files){
    
 Convert(file, dest="h5seurat",
    
    assay = "RNA",
    
       overwrite=F)
    
 }
    
    
    
    
    R
    
    
![](https://ad.itadn.com/c/weblog/blog-img/images/2025-08-16/WE28tn5kmY0KGjifJTSNZCBvchX1.png)