def action(args):
dbname = args.database_file
pth, fname = path.split(dbname)
zip_dest = args.download_dir or pth or '.'
zfile, downloaded = ncbi.fetch_data(
dest_dir = zip_dest,
clobber = args.clobber)
if not os.access(dbname, os.F_OK) or args.clobber:
log.warning('creating new database in %s using data in %s' % \
(dbname, zfile))
con = ncbi.db_connect(dbname, clobber=True)
with con:
ncbi.db_load(con, zfile)
if not args.preserve_inconsistent_taxonomies:
curs = con.cursor()
curs.execute("""
UPDATE nodes
SET rank = 'no_rank'
WHERE tax_id IN (SELECT n1.tax_id
FROM nodes n1
JOIN nodes n2
ON n1.parent_id = n2.tax_id
WHERE n1.rank = n2.rank
AND n1.rank NOT IN ('root', 'no_rank'))
""")
con.close()
else:
log.warning('taxonomy database already exists in %s' % dbname)
def action(args):
dbname = args.database_file
pth, fname = path.split(dbname)
zip_dest = args.download_dir or pth or '.'
zfile, downloaded = ncbi.fetch_data(
dest_dir = zip_dest,
clobber = args.clobber)
if not os.access(dbname, os.F_OK) or args.clobber:
log.warning('creating new database in %s using data in %s' % \
(dbname, zfile))
con = ncbi.db_connect(dbname, clobber=True)
ncbi.db_load(con, zfile)
con.close()
else:
log.warning('taxonomy database already exists in %s' % dbname)
