mapFileUUID2submitterID.py

#!/usr/bin/python
#-*- coding:utf-8 -*-
################################################
#File Name: mapFileUUID2submitterID.py
#Author: C.J. Liu
#Mail: samliu@hust.edu.cn
#Created Time: Tue 15 Nov 2016 03:53:10 PM CST
################################################



import os,sys
import requests
import json
import argparse

def usage():
	description = '''
	Problem: 
		I choose project BRCA on GDC(https://gdc-portal.nci.nih.gov/projects/t) and forward to WXS(1,050 cases, 2,175 bam files). Download manifest file from the summary tab. In fact the manifest only contains the file_id, file_name and md5. I can't tell sample information like TCGA barcode. On the Files tab in the search result of GDC-Portal, we can download sample information in form of json in some condition. However, I can't get sample information from the BRCA-WXS json file. Use GDC-API files endpoint.
	Task: 
		Map file_id to sample sample id through GDC-API (https://gdc-docs.nci.nih.gov/API/Users_Guide/Search_and_Retrieval/#filters-specifying-the-quer
	'''
	usage = """%(prog)s -i <manifest.txt>"""
	parser = argparse.ArgumentParser(description = description, usage = usage)
	
	parser.add_argument("-i", "--input", dest = 'manifest', type = str, help = "Input manifest file downloaded from gdc-portal or file contains first column as file_id", required = True)
	parser.add_argument('-v','--version',action='version', version='%(prog)s 1.0')
	
	args = parser.parse_args()
	return args

def loadManifest(manifest):
	file_ids = list()
	with open(manifest, 'r') as foo:
		for line in foo:
			arr = line.rstrip().split("\t")
			if len(arr[0]) != 36: continue
			file_ids.append(arr[0])
	return file_ids

def makeParams(file_ids):
	params ={
		"filters":{
			"op":"in",
			"content":{
				"field":"files.file_id",
				"value":file_ids
			}
		},
    "format":"TSV",
    "fields":"file_id,file_name,cases.case_id,cases.submitter_id,cases.samples.sample_id,cases.samples.submitter_id,cases.samples.portions.analytes.aliquots.aliquot_id,cases.samples.portions.analytes.aliquots.submitter_id,cases.samples.sample_type,cases.samples.tissue_type,data_category,data_type",#The must be no space after comma
	"size":len(file_ids)
	}
	return params
	
def gdcAPI(file_ids, manifest):
	output = manifest + '.map2submitterID'
	outputh = open(output, 'w')
	files_endpt = "https://api.gdc.cancer.gov/files"
	params = makeParams(file_ids)
	response = requests.post(files_endpt, json = params)
	outputh.write(response.text)
	outputh.close()
	# print(response.text)
	
def run(manifest):
	file_ids = loadManifest(manifest)
	gdcAPI(file_ids, manifest)
	
def main():
	args = usage()
	run(args.manifest)

if __name__ == '__main__':
	main()