602panel_test/s02_samplefile_v0_20220915_finish.py

#####
#将样本信息分别到不同的目录下
####
import pandas as pd
import xlrd
import os,sys
import argparse

####creat the analysis
def analis_dir(inputpath,laneid):
	#新建出报告的目录
	pancancer_dir = os.path.join('/cgdata/pancancer_report', laneid)
	if not os.path.exists(pancancer_dir):
		os.mkdir(pancancer_dir)
	svdir1 = os.path.join(inputpath, '1SV_varscan_pair')
	if not os.path.exists(svdir1):
		os.mkdir(svdir1)
	svdir2= os.path.join(inputpath, '1SV_vardict_pair')
	if not os.path.exists(svdir2):
		os.mkdir(svdir2)
	# for CNV
	CNVdir = os.path.join(inputpath, '2CNV_cnvkit_pair')
	if not os.path.exists(CNVdir):
		os.mkdir(CNVdir)
	# for MSI
	MSI_dir = os.path.join(inputpath, '3MSI_msisensor2_pair')
	if not os.path.exists(MSI_dir):
		os.mkdir(MSI_dir)
	# for germline result
	gemerlinedir = os.path.join(inputpath, '4Germline_unpair')
	if not os.path.exists(gemerlinedir):
		os.mkdir(gemerlinedir)
	# for HL result
	HLdir = os.path.join(inputpath, '5HL_gatk_unpair')
	if not os.path.exists(HLdir):
		os.mkdir(HLdir)
	# for fusion
	fusion_method1_dir = os.path.join(inputpath, '6Fusion_manta_pair')
	if not os.path.exists(fusion_method1_dir):
		os.mkdir(fusion_method1_dir)
	fusion_method2_dir = os.path.join(inputpath, '6Fusion_genefusion_unpair')
	if not os.path.exists(fusion_method2_dir):
		os.mkdir(fusion_method2_dir)
	#for HLA
	HLA_dir = os.path.join(inputpath, '7HLA-HD_unpair')
	if not os.path.exists(HLA_dir):
		os.mkdir(HLA_dir)
	# for qc
	qc_dir = os.path.join(inputpath, '8Fastqc')
	if not os.path.exists(qc_dir):
		os.mkdir(qc_dir)
	# for ontarget
	ontarget_dir = os.path.join(inputpath, '9Ontarget')
	if not os.path.exists(ontarget_dir):
		os.mkdir(ontarget_dir)
	# for coverage
	coverage_dir = os.path.join(inputpath, '10Coverage')
	if not os.path.exists(coverage_dir):
		os.mkdir(coverage_dir)
	# datasummary
	datasummary_dir = os.path.join(inputpath, 'datasummary')
	if not os.path.exists(datasummary_dir):
		os.mkdir(datasummary_dir)



def tumortyple(inputpath,laneid):
	sampledir = os.path.join(inputpath, laneid + '_sample_infor_label.txt')
	sampleinfor = pd.read_table(sampledir, sep='\t', header=0)
	for i in range(len(sampleinfor)):
		sample = sampleinfor.loc[i, 'samplename']
		# make the result dir
		result_dir = os.path.join(inputpath, 'resultfile')
		if not os.path.exists(result_dir):
			os.mkdir(result_dir)
		sample_dir = os.path.join(result_dir, sample)
		if not os.path.exists(sample_dir):
			os.mkdir(sample_dir)
		sampledata = pd.DataFrame()
		sampledata.loc[0, 'sampleid'] = sample
		sampledata.loc[0, 'tumortype'] = sampleinfor.loc[i, 'tumortype']
		outputfile = os.path.join(sample_dir, laneid + '-' + sample + '.tumortype.xlsx')
		writer = pd.ExcelWriter(outputfile)
		sampledata.to_excel(writer, sheet_name='tumortype', index=False)
		writer.save()
		writer.close()

def tumortyperunmain(inputpath,laneid):
	analis_dir(inputpath,laneid)
	tumortyple(inputpath,laneid)



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

if __name__=='__main__':
	parser = argparse.ArgumentParser(description='sample infor for tumortype')
	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
	tumortyperunmain(Inputpath,Laneid)