从分析结果中根据list提取突变信息

本文主要是介绍从分析结果中根据list提取突变信息，希望对大家解决编程问题提供一定的参考价值，需要的开发者们随着小编来一起学习吧！

# _*_coding:utf-8_*_
# author: 稻田工作者
# date: 2020-06-13"""根据原始样本对应的突变信息从数据分析文件中提取检出结果，如：
原始样本LC-BR3对应的突变信息如下：
NM_000245.2:exon14_intron14:c.3028_3028+16del17:p.?
NM_005228.3:exon20:c.2290_2291ins12:p.A763_Y764insFQEA
NM_000245.2:intron13:c.2888-41_2888-2delTAGCCGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAA:p.?
即：需要从分析文件中提取该突变信息对应的sample_name,Depth,frequency,CDS_change,Var_ss对应的文件内index(0,9,10,14,28)
"""import xlrd
import csv
import pandas as pd# 根据样本对应突变list生成样本和突变的字典
def generate_sample_dict(work_path,mutation_dict):list_file = open(r"%s\list.txt"%work_path,"r")for line in list_file:s_key = line.strip().split("\t")[0]s_value = line.strip().split("\t")[1]if s_value is not '':if s_key in mutation_dict:mutation_dict.get(s_key).append(s_value)else:mutation_dict.setdefault(s_key,[]).append(s_value)return mutation_dictdef extract_info(work_path,data_xlxs_name,mutation_dict):data_xlxs = xlrd.open_workbook(r"%s\%s.xlsx"%(work_path,data_xlxs_name),"r")data_sheet = data_xlxs.sheet_by_name("SNVIndelHotSpot")n_rows = data_sheet.nrows# 遍历源数据文件和样本list信息提取数据with open(r"%s\%s_filter_data.csv"%(work_path,data_xlxs_name),"w",newline="")as outfile:header = ["#sample_name","Depth","frequency","CDS_change","Var_ss"]write_csv = csv.DictWriter(outfile,fieldnames=header)write_csv.writeheader()for n in range(1,n_rows):if data_sheet.cell(n,14).value in mutation_dict and mutation_dict.values(data_sheet.cell(n,14).value) in data_sheet.cell(n,0).value:for k,v in mutation_dict.items():if k in data_sheet.cell(n,0).value and data_sheet.cell(n,14).value in v:write_csv.writerow({"#sample_name":data_sheet.cell(n,0).value,"Depth":data_sheet.cell(n,9).value,"frequency":data_sheet.cell(n,10).value,"CDS_change":data_sheet.cell(n,14).value,"Var_ss":data_sheet.cell(n,28).value})
def csv2xls(work_path,data_xlxs_name):csv_file = pd.read_csv(r"%s\%s_filter_data.csv"%(work_path,data_xlxs_name),encoding="utf-8",index_col=0,engine='python')csv_file.to_excel(r"%s\%s_filter_data.xlsx"%(work_path,data_xlxs_name),sheet_name="filter_data")if __name__ == '__main__':mutation_dict = {}work_path = input("输入list及源分析文件路径: ")generate_sample_dict(work_path,mutation_dict)data_xlxs_name = input("输入需要提取数据的源文件名称：")extract_info(work_path,data_xlxs_name,mutation_dict)csv2xls(work_path, data_xlxs_name)

 

这篇关于从分析结果中根据list提取突变信息的文章就介绍到这儿，希望我们推荐的文章对编程师们有所帮助！

---