comparison ete_init_taxdb.py @ 15:1e85af7a29c4 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty

14:d40b9a7debe5

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)

15:1e85af7a29c4

import optparse
from urllib.request import urlretrieve

from ete3.ncbi_taxonomy.ncbiquery import update_db

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 create",
)
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(
        "https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", "taxdump.tar.gz"
    )
    taxdump = "taxdump.tar.gz"

update_db(dbfile=options.database, targz_file=taxdump)