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Commit message:
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modified:
config_lookup config_lookup.py |
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added:
._README.rst ._accession_lists_links.txt ._config_lookup ._glassgo_macros.xml ._glassgo_wrapper.xml ._test-data test-data/._NsiR4_Synechocystis_sp_PCC6803.fa test-data/._glassgo_NsiR4_Synechocystis_sp_PCC6803.fa tool-data/._.DS_Store tool-data/._glassgo_accession_list.txt |
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removed:
config_lookup/config_lookup.py config_lookup/dist/config_lookup config_lookup/tmpnJ2yER |
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| diff -r 8867b84faf51 -r 38f4e50850ca config_lookup/config_lookup.py --- a/config_lookup/config_lookup.py Thu Jan 16 02:34:33 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,75 +0,0 @@ -#!/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', required=True, 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() - - # ./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() |
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