Mercurial > repos > earlhaminst > ete
comparison ete_init_taxdb.py @ 2:03c10736e497 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
| author | earlhaminst |
|---|---|
| date | Tue, 07 Nov 2017 11:45:13 -0500 |
| parents | |
| children |
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| 1:a4ba317fc713 | 2:03c10736e497 |
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| 1 import optparse | |
| 2 | |
| 3 import ete3.ncbi_taxonomy | |
| 4 from six.moves.urllib.request import urlretrieve | |
| 5 | |
| 6 parser = optparse.OptionParser() | |
| 7 parser.add_option('-t', '--taxdump', dest='taxdump', default=None, | |
| 8 help='NCBI taxdump (tar.gz) will be downloaded if not given') | |
| 9 parser.add_option('-d', '--database', dest="database", default=None, | |
| 10 help='ETE sqlite data base to use (default: ~/.etetoolkit/taxa.sqlite)') | |
| 11 options, args = parser.parse_args() | |
| 12 if options.database is None: | |
| 13 parser.error("-d option must be specified") | |
| 14 if options.taxdump is not None: | |
| 15 taxdump = options.taxdump | |
| 16 else: | |
| 17 urlretrieve("http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", "taxdump.tar.gz") | |
| 18 taxdump = "taxdump.tar.gz" | |
| 19 | |
| 20 # will remove a taxdump.tar.gz file at the end | |
| 21 # which will lead to an errmessage if not present | |
| 22 # if the tool is run on a taxdump in the current dir it will be | |
| 23 # deleted in the end | |
| 24 ete3.ncbi_taxonomy.ncbiquery.update_db(dbfile=options.database, targz_file=taxdump) |