602panel_test/d1_datasummary_QC.py

import pandas as pd
import os,sys
import argparse


def ontarget_sum(inputpath):
	#inputpath = '/cgdata/bioproject/pancancer602gene/CGB0329'
	laneid = inputpath.split('/')[-1]
	QCsumdir = '/cgdata/bioproject/pancancer602gene/NGS_QC_602pancancer'
	outputdir = os.path.join(QCsumdir, laneid)
	if not os.path.exists(outputdir):
		os.mkdir(outputdir)
	tempfile = os.path.join(inputpath, 'tempfile')
	QCdir = os.path.join(tempfile, 'QC')
	# 对目录下所有的ontarget.txt进行汇总
	files = os.listdir(QCdir)
	ontargetfile = [s for s in files if s.endswith('ontarget.txt')]
	targetsum = pd.DataFrame()
	for i in range(len(ontargetfile)):
		sampledir = os.path.join(QCdir, ontargetfile[i])
		sampleQC = pd.read_table(sampledir, sep='\t', header=0)
		targetsum = sampleQC.append(targetsum)
	cols = ['sampleid', 'Total_Read(M)', 'Map(%)', 'T_size', 'On_Target(%)', 'T_Dup(%)', 'T_Mean', 'Insert_Size', 'SD',
			'Fold80', '>1X', '>20X', '>30X', '>50X', '>100X', '>300X', 'Adjust_30X']
	targetsum = targetsum[cols]
	#输出结果
	targetoutput = os.path.join(outputdir, laneid + '_' + 'target_sum.txt')
	targetsum.to_csv(targetoutput, sep='\t', header=True, index=False)



def report_sum(inputpath):
	# inputpath = '/cgdata/bioproject/pancancer602gene/CGB0329'
	laneid = inputpath.split('/')[-1]
	QCsumdir = '/cgdata/bioproject/pancancer602gene/NGS_QC_602pancancer'
	outputdir = os.path.join(QCsumdir, laneid)
	if not os.path.exists(outputdir):
		os.mkdir(outputdir)
	tempfile = os.path.join(inputpath, 'tempfile')
	QCdir = os.path.join(tempfile, 'QC')
	###对目录下所有的report QC进行汇总
	files = os.listdir(QCdir)
	reportfile = [s for s in files if s.endswith('_qc_report.txt')]
	reportsum = pd.DataFrame()
	for i in range(len(reportfile)):
		sampledir = os.path.join(QCdir, reportfile[i])
		sample_report = pd.read_table(sampledir, sep='\t', header=0)
		reportsum = sample_report.append(reportsum)
	#output the result
	reportoutput = os.path.join(outputdir, laneid + '_report_sum.txt')
	reportsum.to_csv(reportoutput, sep='\t', header=True, index=False)



def run(inputpath):
	ontarget_sum(inputpath)
	report_sum(inputpath)


if __name__=='__main__':
	parser = argparse.ArgumentParser(description='QC sum')
	parser.add_argument('-i', '--inputpath', type=str, help='the path of lane')
	args = parser.parse_args()
	Inputpath = args.inputpath
	run(Inputpath)