Capablezzm
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Scanpy单细胞处理流程之一：数据读取

第一步：确定自己的环境配置，并且导入相应的模块

本人的所用模块版本信息如下所示： （待补充以下： 1：h5ad的数据结构 2：环境信息 3：其他的读取形式）

#安装导入需要的模块
import numpy as np
import pandas as pd
import scanpy as sc
import os
import torch
import omicverse

/home/zhaozm/anaconda3/envs/sccell/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
  warnings.warn(msg, FutureWarning)
/home/zhaozm/anaconda3/envs/sccell/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_excel from `anndata` is deprecated. Import anndata.io.read_excel instead.
  warnings.warn(msg, FutureWarning)
/home/zhaozm/anaconda3/envs/sccell/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_hdf from `anndata` is deprecated. Import anndata.io.read_hdf instead.
  warnings.warn(msg, FutureWarning)
/home/zhaozm/anaconda3/envs/sccell/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
  warnings.warn(msg, FutureWarning)
/home/zhaozm/anaconda3/envs/sccell/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_mtx from `anndata` is deprecated. Import anndata.io.read_mtx instead.
  warnings.warn(msg, FutureWarning)
/home/zhaozm/anaconda3/envs/sccell/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  warnings.warn(msg, FutureWarning)
/home/zhaozm/anaconda3/envs/sccell/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_umi_tools from `anndata` is deprecated. Import anndata.io.read_umi_tools instead.
  warnings.warn(msg, FutureWarning)



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  / __ \____ ___  (_)___| |  / /__  _____________ 
 / / / / __ `__ \/ / ___/ | / / _ \/ ___/ ___/ _ \ 
/ /_/ / / / / / / / /__ | |/ /  __/ /  (__  )  __/ 
\____/_/ /_/ /_/_/\___/ |___/\___/_/  /____/\___/                                              

Version: 1.6.2, Tutorials: https://omicverse.readthedocs.io/

# 检查当前的工作路径
current_working_directory = os.getcwd()
print(f"当前的工作路径: {current_working_directory}")

# 检查 torch 的 GPU 版本
if torch.cuda.is_available():
    print(f"torch GPU 版本: {torch.version.cuda}")
else:
    print("未检测到 GPU")

当前的工作路径: /mnt/DEV_8T/zhaozm/scanpy_单细胞流程/pbmc_test
torch GPU 版本: 12.1

## 读取文件
adata = sc.read_10x_mtx(
    "../filtered_gene_bc_matrices/hg19/",  # the directory with the `.mtx` file
    var_names="gene_symbols",  # use gene symbols for the variable names (variables-axis index)
    cache=True,  # write a cache file for faster subsequent reading
)

adata

AnnData object with n_obs × n_vars = 2700 × 32738
    var: 'gene_ids'

## 保存为h5ad格式
adata.write('pbmc3k.h5ad')

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