annotate config_lookup/config_lookup.py @ 17:0694c93739bf draft

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1 #!/usr/local/bin/python3
2 
3 '''
4 This script downloads lookup tables and integrates these into the Galaxy instance
5 
6 USAGE 
7 		config_lookup.py --galaxy GALAXY --acclinks ACCLINKS [--acclists ACCLISTS]
8 
9 OPTIONS 
10 		-h, --help           show this help message and exit
11 
12 '''
13 
14 import os
15 import argparse
16 import requests
17 import sys
18 import shutil
19 
20 
21 def main():
22 	# parse arguments
23 	parser = argparse.ArgumentParser(description='incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches')
24 	parser.add_argument('--galaxy', required=True, help='(absolute) path to the root directory of the Galaxy instance')
25 	parser.add_argument('--acclinks', required=True, help='(absolute) path to file containing URLs to the accession lists')
26 	parser.add_argument('--acclists', help='(absolute) path to directory to save the accession lists to')
27 	args = parser.parse_args()
28 
29 	# ./acclists as default folder for the accession lists
30 	if args.acclists == None:
31 		args.acclists = os.path.join(os.getcwd(),'acclists')
32 
33 	# check for existence of the folders for galaxy and URLs to the accession lists
34 	if not os.path.exists(args.galaxy):
35 		print('\tERROR: ' + args.galaxy + ' could not be found!')
36 		sys.exit()	
37 	if not os.path.exists(args.acclinks):
38 		print('\tERROR: ' + args.acclinks + ' could not be found!')
39 		sys.exit()
40 
41 	print('################ configure the accession lists ################')
42 	print('### the accession lists will be saved to ' + args.acclists)
43 
44 	# create folder for accession lists
45 	if not os.path.exists(args.acclists):
46 		os.makedirs(args.acclists)
47 
48 	# 
49 	with open(args.acclinks, 'r') as link:
50 		# create list with lookup tables that populates the user interface
51 		accDataTableFile = os.path.join(os.getcwd(),'tool-data/glassgo_accession_list.txt')
52 		
53 		accDataTable = open(accDataTableFile,'w')
54 		accDataTable.write('global\tglobal\n')
55 		# fetch accession lists 
56 		for url in link:
57 			acc = requests.get(url)
58 			filename = str(os.path.basename(url)).replace('\n','')
59 			print('### fetch: ' + filename)
60 			open(os.path.join(args.acclists,filename),'wb').write(acc.content)
61 			
62 			# 
63 			accDataTable.write(filename + '\t')
64 			accDataTable.write(os.path.join(args.acclists,filename) + '\n')
65 
66 		accDataTable.close()
67 		print('### create tab-separated list '+ accDataTableFile)
68 
69 		# move list with accession list to /galaxy/tool-data
70 		shutil.copy(accDataTableFile,os.path.join(args.galaxy,'tool-data/'))
71 		print('### move tab-separated list to ' + str(os.path.join(args.galaxy,'tool-data/')))
72 		
73 # 
74 if __name__ == "__main__":
75 	main()