changeset 15:4ac32c671a40 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config_lookup.py	Wed Jan 15 13:34:02 2020 -0500
@@ -0,0 +1,79 @@
+#!/usr/local/bin/python3
+
+'''
+This script downloads lookup tables and integrates these into the Galaxy instance
+
+USAGE 
+		config_lookup.py --galaxy GALAXY --acclinks ACCLINKS [--acclists ACCLISTS]
+
+OPTIONS 
+		-h, --help           show this help message and exit
+
+'''
+
+import os
+import argparse
+import requests
+import sys
+import shutil
+
+def main():
+	# parse arguments
+	parser = argparse.ArgumentParser(description='incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches')
+	parser.add_argument('--galaxy', required=True, help='(absolute) path to the root directory of the Galaxy instance')
+	parser.add_argument('--acclinks', help='(absolute) path to file containing URLs to the accession lists')
+	parser.add_argument('--acclists', help='(absolute) path to directory to save the accession lists to')
+	args = parser.parse_args()
+
+
+	# ./accession_lists_links.txt as default
+	if args.acclinks == None:
+		args.acclinks = os.path.join(os.getcwd(), 'accession_lists_links.txt')
+
+	# ./acclists as default folder for the accession lists
+	if args.acclists == None:
+		args.acclists = os.path.join(os.getcwd(),'acclists')
+
+	# check for existence of the folders for galaxy and URLs to the accession lists
+	if not os.path.exists(args.galaxy):
+		print('\tERROR: ' + args.galaxy + ' could not be found!')
+		sys.exit()	
+	if not os.path.exists(args.acclinks):
+		print('\tERROR: ' + args.acclinks + ' could not be found!')
+		sys.exit()
+
+	print('################ configure the accession lists ################')
+	print('### the accession lists will be saved to ' + args.acclists)
+
+	# create folder for accession lists
+	if not os.path.exists(args.acclists):
+		os.makedirs(args.acclists)
+
+	# 
+	with open(args.acclinks, 'r') as link:
+		# create list with lookup tables that populates the user interface
+		accDataTableFile = os.path.join(os.getcwd(),'tool-data/glassgo_accession_list.txt')
+		
+		accDataTable = open(accDataTableFile,'w')
+		accDataTable.write('global\tglobal\n')
+		# fetch accession lists 
+		for url in link:
+			acc = requests.get(url)
+			filename = str(os.path.basename(url)).replace('\n','')
+			print('### fetch: ' + filename)
+			open(os.path.join(args.acclists,filename),'wb').write(acc.content)
+			
+			# 
+			accDataTable.write(filename + '\t')
+			accDataTable.write(os.path.join(args.acclists,filename) + '\n')
+
+		accDataTable.close()
+		print('### create tab-separated list '+ accDataTableFile)
+
+		# move list with accession list to /galaxy/tool-data
+		shutil.copy(accDataTableFile,os.path.join(args.galaxy,'tool-data/'))
+		print('### move tab-separated list to ' + str(os.path.join(args.galaxy,'tool-data/')))
+		
+# 
+if __name__ == "__main__":
+	main()