Mercurial > repos > earlhaminst > ete
view ete_init_taxdb.py @ 8:16e925bf567e draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit ed32f2e6d8174873cefcbe141084f857f84b0586"
author | earlhaminst |
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date | Thu, 31 Oct 2019 07:48:59 -0400 |
parents | 03c10736e497 |
children |
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import optparse import ete3.ncbi_taxonomy from six.moves.urllib.request import urlretrieve parser = optparse.OptionParser() parser.add_option('-t', '--taxdump', dest='taxdump', default=None, help='NCBI taxdump (tar.gz) will be downloaded if not given') parser.add_option('-d', '--database', dest="database", default=None, help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)') options, args = parser.parse_args() if options.database is None: parser.error("-d option must be specified") if options.taxdump is not None: taxdump = options.taxdump else: urlretrieve("http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", "taxdump.tar.gz") taxdump = "taxdump.tar.gz" # will remove a taxdump.tar.gz file at the end # which will lead to an errmessage if not present # if the tool is run on a taxdump in the current dir it will be # deleted in the end ete3.ncbi_taxonomy.ncbiquery.update_db(dbfile=options.database, targz_file=taxdump)