def test_compile_database(self):
me = Database()
me.output = self.tmpdir
# don't compile
me.compile = 'none'
me.compile_database()
self.assertListEqual(listdir(self.tmpdir), [])
# get database files
copy(join(self.datadir, 'DnaK', 'linear.faa'),
join(self.tmpdir, 'db.faa'))
copy(join(self.datadir, 'DnaK', 'prot2tid.txt'),
join(self.tmpdir, 'taxon.map'))
makedirs(join(self.tmpdir, 'taxdump'))
copy(join(self.datadir, 'DnaK', 'taxdump', 'nodes.dmp'),
join(self.tmpdir, 'taxdump', 'nodes.dmp'))
copy(join(self.datadir, 'DnaK', 'taxdump', 'names.dmp'),
join(self.tmpdir, 'taxdump', 'names.dmp'))
with open(join(self.tmpdir, 'taxon.map'), 'r') as f:
me.taxonmap = dict(x.split('\t') for x in f.read().splitlines())
# set parameters
me.threads = 1
me.tmpdir = self.tmpdir
me.makeblastdb = 'makeblastdb'
me.diamond = 'diamond'
# compile blast database
me.compile = 'blast'
me.compile_database()
self.assertTrue(isdir(join(self.tmpdir, 'blast')))
for ext in ('phr', 'pin', 'pog', 'psd', 'psi', 'psq'):
self.assertTrue(isfile(join(self.tmpdir, 'blast', f'db.{ext}')))
rmtree(join(self.tmpdir, 'blast'))
# compile diamond database
me.compile = 'diamond'
me.compile_database()
self.assertTrue(isdir(join(self.tmpdir, 'diamond')))
self.assertTrue(isfile(join(self.tmpdir, 'diamond', 'db.dmnd')))
rmtree(join(self.tmpdir, 'diamond'))
# compile both databases
me.compile = 'both'
me.compile_database()
self.assertTrue(isdir(join(self.tmpdir, 'blast')))
for ext in ('phr', 'pin', 'pog', 'psd', 'psi', 'psq'):
self.assertTrue(isfile(join(self.tmpdir, 'blast', f'db.{ext}')))
self.assertTrue(isdir(join(self.tmpdir, 'diamond')))
self.assertTrue(isfile(join(self.tmpdir, 'diamond', 'db.dmnd')))
rmtree(join(self.tmpdir, 'blast'))
rmtree(join(self.tmpdir, 'diamond'))
# clean up
remove(join(self.tmpdir, 'db.faa'))
remove(join(self.tmpdir, 'taxon.map'))
rmtree(join(self.tmpdir, 'taxdump'))
def test_build_diamond_db(self):
me = Database()
me.output = self.tmpdir
me.diamond = 'diamond'
me.threads = 1
me.tmpdir = self.tmpdir
copyfile(join(self.datadir, 'DnaK', 'linear.faa'),
join(self.tmpdir, 'db.faa'))
with open(join(self.datadir, 'DnaK', 'prot2tid.txt'), 'r') as f:
me.taxonmap = dict(x.split('\t') for x in f.read().splitlines())
makedirs(join(self.tmpdir, 'taxdump'))
copyfile(join(self.datadir, 'DnaK', 'taxdump', 'nodes.dmp'),
join(self.tmpdir, 'taxdump', 'nodes.dmp'))
me.build_diamond_db()
self.assertTrue(isdir(join(self.tmpdir, 'diamond')))
self.assertTrue(isfile(join(self.tmpdir, 'diamond', 'db.dmnd')))
rmtree(join(self.tmpdir, 'diamond'))
remove(join(self.tmpdir, 'db.faa'))
remove(join(self.tmpdir, 'taxdump', 'nodes.dmp'))
