602panel_test/s03_datasoftlink_20220915_finish.py

import pandas as pd
import os,sys
import re
import argparse
def subdir_list(dirname):
	"""获取目录下所有子目录名
	@param dirname: str 目录的完整路径
	@return: list(str) 所有子目录完整路径组成的列表
	"""
	return list(filter(os.path.isdir,
		map(lambda filename: os.path.join(dirname, filename),
			os.listdir(dirname))))

def file_list(dirname, ext='.gz'):
	"""获取目录下所有特定后缀的文件
	@param dirname: str 目录的完整路径
	@param ext: str 后缀名, 以点号开头
	@return: list(str) 所有子文件名(不包含路径)组成的列表
	"""
	return list(filter(
		lambda filename: os.path.splitext(filename)[1] == ext,
		os.listdir(dirname)))


def linkfile(inputpath,file0,tumor_fastq,tumor_project):
	tumorfile = [s for s in file0 if tumor_fastq in s]
	for j in range(len(tumorfile)):
		files_tumor = tumorfile[j]
		files_tumor_name = files_tumor.split('-')[-1]
		if files_tumor_name == tumor_fastq:
			file1 = file_list(files_tumor, ext='.gz')
			for m in range(len(file1)):
				file1_0 = file1[m]
				Rlabel = file1_0.split('_')[-1]
				samplenew = tumor_project + '_' + Rlabel
				samplenew_dir = os.path.join(inputpath, samplenew)
				sampleold_dir = os.path.join(files_tumor, file1_0)
				linkcmd = 'ln -s ' + sampleold_dir + ' ' + samplenew_dir
				os.system(linkcmd)


def linkmain(inputpath,laneid,bclpath):
	file0 = subdir_list(bclpath)
	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)):
		# for the tumor
		case_project = sampleinfor.loc[i, 'tumor']
		case_fastq = sampleinfor.loc[i, 'fastq_tumor']
		linkfile(inputpath,file0, case_fastq, case_project)
		# for the normal
		normal_project = sampleinfor.loc[i, 'normal']
		normal_fastq = sampleinfor.loc[i, 'fastq_normal']
		linkfile(inputpath,file0, normal_fastq, normal_project)



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')
	parser.add_argument('-f', '--bclpath', type=str, help='the fastq file')
	args = parser.parse_args()
	Inputpath = args.inputpath
	Laneid = args.laneid
	Bclpath=args.bclpath
	linkmain(Inputpath,Laneid,Bclpath)