| Previous changeset 14:f89e35286285 (2020-01-14) Next changeset 16:acbcdd5b4c60 (2020-01-15) |
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Commit message:
Uploaded |
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added:
config_lookup.py |
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| diff -r f89e35286285 -r 4ac32c671a40 config_lookup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config_lookup.py Wed Jan 15 13:34:02 2020 -0500 |
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| @@ -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() |