def main(args):
if not args:
if ask('Download latest ncbi taxonomy dump file?', ['y', 'n']) == 'y':
status = os.system('wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz')
if status == 0:
update('taxdump.tar.gz')
else:
fname = ask_filename('path to tar.gz file containing ncbi taxonomy dump:')
update(fname)
else:
update(args[0])
CREATE TABLE merged (taxid_old INT, taxid_new INT);
CREATE INDEX spname1 ON species (spname COLLATE NOCASE);
CREATE INDEX spname2 ON synonym (spname COLLATE NOCASE);
.separator '\t'
.import taxa.tab species
.import syn.tab synonym
.import merged.tab merged
"""
CMD.write(cmd)
CMD.close()
os.system("sqlite3 taxa.sqlite < commands.tmp")
os.system("rm syn.tab merged.tab taxa.tab commands.tmp")
print "Creating extended newick file with the whole NCBI tree [ncbi.nw]"
t.write(outfile="ncbi.nw", features=["name", "taxname"])
if __name__ == '__main__':
if len(sys.argv) == 1:
if ask('Download latest ncbi taxonomy dump file?', ['y', 'n']) == 'y':
status = os.system('wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz')
if status == 0:
update('taxdump.tar.gz')
else:
fname = ask_filename('path to tar.gz file containing ncbi taxonomy dump:')
update(fname)
else:
update(sys.argv[1])
