如何依照靶点名称,找到chembl数据库中的相关实验数据

chembl提供了API(chembl_webresource_client)可以用来获取数据
安装一下:

pip install chembl_webresource_client

废话少说,上代码:

import pandas as pd
from chembl_webresource_client.new_client import new_client
import argparse

parser = argparse.ArgumentParser(description="get chembl activities infomation of a special target")
parser.add_argument('--gene_name',  '-g' , required=True, type=str,  help='gene name of a interestd target ') 
parser.add_argument('--output',  '-o' , required=True, type=str,  help='output file path(csv)')   
args = parser.parse_args()
gene_name =  args.gene_name
output = args.output


def activities(gene_name,out_file):
    """    
    Parameters
    ----------
    gene_name : str
        the name of target 
    out_file : TYPE
        output file path

    Returns
    -------
    None.

    """
    
    target = new_client.target
    activity = new_client.activity
    parp = target.search(gene_name)[0]
    parp_activities = activity.filter(target_chembl_id=parp['target_chembl_id'])
    
    
    df = pd.DataFrame(parp_activities)
    df.to_csv(out_file,index=False)

activities(gene_name,output)

使用方式是 xxx.py -g 基因名 -o 输出文件路径(csv)