602panel_test/s01_samplesheet_v0_20230420_finish.py

# -*- encoding: utf-8 -*-
'''
@File    :   s01_samplesheet_v0_20230420_finish.py
@Time    :   2023/04/20 11:35:55
@Author  :   liuxiangqiong 
@Version :   0.1
'''

# here put the import lib

import pandas as pd
import os
import argparse
import re

##项目表有上海和启动两个sheet
##修改，提取检测项目的编号，204或者602.
def pancancer_project(inputpath,laneid):
	#inputpath = '/cgdata/liuxiangqiong/work62pancancer/pipelinetest-CGB0158'
	#laneid = 'CGB0158'
	###0.拷贝CNV分级表
	rawcnvdir = '/cgdata/pancancer_report/refdata/CNV.xlsx'
	cnvtable = pd.read_excel(rawcnvdir)
	cnvtable['gene'] = cnvtable['gene'].str.strip()
	cnvtable['CNV_label'] = cnvtable['CNV_label'].str.strip()
	refcnvdir1 = '/cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/CNV_tier_infor.txt'
	biocnvdir2 = '/cgdata/bioproject/pancancer602gene/Project_table/CNV_tier_infor.txt'
	cnvtable.to_csv(refcnvdir1, index=False, header=True, sep='\t')
	cnvtable.to_csv(biocnvdir2, index=False, header=True, sep='\t')
	###1.从项目表提取出当前大panel的样本表
	project = pd.read_excel('/cgdata/bioproject/pancancer602gene/Project_table/阅尔基因项目信息总表-0606.xlsx',engine='openpyxl',sheet_name=None)
	#project = pd.read_excel('/cgdata/liuxiangqiong/work62pancancer/probe204/阅尔基因项目信息总表-0606.xlsx',engine='openpyxl',sheet_name=None)
	#提取出两个sheet的结果并追加合并
	project_SH=project['项目信息表-上海']
	project_QD=project['项目信息表-启东']
	project_all=project_QD.append(project_SH)
	project_all.reset_index(drop=True,inplace=True)
	###2.1获得602的项目
	projectsample1 = project_all[project_all['检测项目1'] == '阅全-泛癌种602基因检测']
	projectsample2 = project_all[project_all['检测项目1'].str.contains('CPS', na=False)]
	projectsample_602=projectsample1.append(projectsample2)
	##2.2获得204的项目
	projectsample_204 = project_all[project_all['检测项目1'].str.contains('CMS', na=False)]
	##2.3将204和602项目合并
	projectsample=projectsample_602.append(projectsample_204)
	projectsample.reset_index(drop=True,inplace=True)
	outputfile1 = os.path.join('/cgdata/bioproject/pancancer602gene/Project_table/pancancer_allsamples.xlsx')
	#outputfile1 = os.path.join('/cgdata/bioproject/pancancer602gene/Project_table/pancancer_602gene_samples.xlsx')
	writer = pd.ExcelWriter(outputfile1)
	projectsample.to_excel(writer, sheet_name='sample', index=False)
	writer.save()
	writer.close()
	####3.提取出当前我们panel分析样本的信息
	selectlist = ['样本编号', '样本类型', '临床诊断','检测项目1']
	selectsample = projectsample[selectlist]
	selectsample.reset_index(drop=True, inplace=True)
	selectsample['样本编号'] = selectsample['样本编号'].str.replace("^A", "Lib")
	###3.1 我们从底层表中获取疾病的名称
	tumordbdir = '/cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/TCGA_tumor_list_20220915.txt'
	tumordblist = pd.read_table(tumordbdir, sep='\t', header=0, encoding='gbk')
	# 添加TCGA的名称
	selectsample.rename(columns={'临床诊断': 'tumor_name', '样本编号': 'sampleid', '样本类型': 'sampletype','检测项目1':'project'}, inplace=True)
	selectsample_TCGA = pd.merge(selectsample, tumordblist, on=['tumor_name'], how='left')
	# 将不在TCGA的癌症名称标为unknown
	selectsample_TCGA['tumor_name'] = selectsample_TCGA['tumor_name'].fillna('unknown')
	# 3.2 获得当前的样本对应的信息
	####提取出当前lane的样本对应的信息
	lane_sampelelist = pd.read_table(os.path.join(inputpath, laneid + '_sample.txt'), sep='\t', header=None, names=['sampleid'])
	lane_sampleinfor = pd.merge(lane_sampelelist, selectsample_TCGA, on=['sampleid'], how='left')
	# 输出原始信息表
	outputfile2 = os.path.join(inputpath, laneid + '_sampleinfor_raw.xlsx')
	writer = pd.ExcelWriter(outputfile2)
	lane_sampleinfor.to_excel(writer, sheet_name='sampleinfor', index=False)
	writer.save()
	writer.close()
	return lane_sampleinfor

#inputpath='/cgdata/liuxiangqiong/work62pancancer/probe204'
#laneid='CGB0434_2'
#rawsheet=pancancer_project(inputpath,laneid)

##修改，加上检测项目编号
#且给出下机数据的样本编号。如果对应的需要修改，那么人工再改
def project_pair(rawsheet):
	#inputfile = os.path.join(inputpath, laneid + '_sampleinfor_raw.xlsx')
	#rawsheet = pd.read_excel(inputfile)
	##首先获得所有的肿瘤样本
	rawsheet_tumorid = rawsheet[rawsheet['sampleid'].str.contains('T')]
	rawsheet_tumorid.reset_index(drop=True, inplace=True)
	###获得肿瘤样本名,构建配对表，因为不管正常如何命名，最后的normal也是根据肿瘤样本名，所以只需要看肿瘤样本名就可
	sample_pair = pd.DataFrame()
	for i in range(len(rawsheet_tumorid)):
		sample = rawsheet_tumorid.loc[i, 'sampleid']
		sampletype1 = rawsheet_tumorid.loc[i, 'sampletype']
		tumortype = rawsheet_tumorid.loc[i, 'Abbr']
		projectid=rawsheet_tumorid.loc[i, 'project']
		sample_pair.loc[i, 'samplename'] = sample
		#判断样本项目
		if 'CPS' in projectid:
			sample_pair.loc[i, 'projectid'] = 'Pan602'
		elif 'CMS' in projectid:
			sample_pair.loc[i,'projectid']='Pan204'
		else:
			sample_pair.loc[i,'projectid']='other'
		#获得normal新命名
		sample_pair.loc[i, 'normal'] = sample + 'CN'
		#判断样本类型和tumor新命名
		if sampletype1 == '血浆':
			sample_pair.loc[i, 'tumor'] = sample + 'CT'
			sample_pair.loc[i, 'sampletype'] = 'blood'
			sample_pair.loc[i, 'tumortype'] = tumortype
			sample_pair.loc[i, 'fastq_tumor'] = sample
			sample_pair.loc[i, 'fastq_normal'] = sample[:-2]+'N'
		elif sampletype1=='外周血':
			sample_pair.loc[i, 'tumor'] = sample + 'CT'
			sample_pair.loc[i, 'sampletype'] = 'blood'
			sample_pair.loc[i, 'tumortype'] = tumortype
			sample_pair.loc[i, 'fastq_tumor'] = sample
			sample_pair.loc[i, 'fastq_normal'] = sample[:-2]+'N'
		else:
			sample_pair.loc[i, 'tumor'] = sample + 'TT'
			sample_pair.loc[i, 'sampletype'] = 'FFPE'
			sample_pair.loc[i, 'tumortype'] = tumortype
			sample_pair.loc[i, 'fastq_tumor'] = sample
			sample_pair.loc[i, 'fastq_normal'] = sample[:-1]+'N'
	return sample_pair


def sheetrunmain(inputpath,laneid):
	lane_sampleinfor=pancancer_project(inputpath,laneid)
	project_sample=project_pair(lane_sampleinfor)
	print('project_sample')
	print(project_sample)
	outputfile = os.path.join(inputpath, laneid + '_sample_infor_label.txt')
	project_sample.to_csv(outputfile,sep='\t',header=True, index=False)
	print('finish')




#inputpath='/cgdata/liuxiangqiong/work62pancancer/pipelinetest-CGB0158'
#laneid='CGB0158'
#sheetrun(inputpath,laneid)

if __name__=='__main__':
	parser = argparse.ArgumentParser(description='sample pair')
	parser.add_argument('-i', '--inputpath', type=str, help='the path of lane')
	parser.add_argument('-l', '--laneid', type=str, help='laneid')
	args = parser.parse_args()
	Inputpath = args.inputpath
	Laneid = args.laneid
	sheetrunmain(Inputpath,Laneid)