def test_genome_lineages(self):
me = Database()
me.output = self.tmpdir
me.taxdump = taxdump_from_text(taxdump_proteo)
data = (
('G1', '1224', ''), # Proteobacteria
('G2', '562', '562'), # Escherichia coli
('G3', '622', '622'), # Shigella dysenteriae
('G4', '548', '548')) # Klebsiella aerogenes
me.df = pd.DataFrame(data, columns=['genome', 'taxid',
'species']).set_index('genome')
for rank in [
'superkingdom', 'kingdom', 'phylum', 'class', 'order',
'family', 'genus'
]:
me.df[rank] = ''
me.genome_lineages()
with open(join(self.tmpdir, 'lineages.txt'), 'r') as f:
obs = dict(x.split('\t') for x in f.read().splitlines())
proteo = 'k__Bacteria; p__Proteobacteria;'
self.assertEqual(obs['G1'], proteo + ' c__; o__; f__; g__; s__')
entero = proteo + ' c__Gammaproteobacteria; o__Enterobacterales;' +\
' f__Enterobacteriaceae;'
self.assertEqual(obs['G2'],
entero + ' g__Escherichia; s__Escherichia coli')
self.assertEqual(obs['G3'],
entero + ' g__Shigella; s__Shigella dysenteriae')
self.assertEqual(obs['G4'],
entero + ' g__Klebsiella; s__Klebsiella aerogenes')
remove(join(self.tmpdir, 'lineages.txt'))
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_blast_db(self):
me = Database()
me.output = self.tmpdir
me.makeblastdb = 'makeblastdb'
copy(join(self.datadir, 'DnaK', 'linear.faa'),
join(self.tmpdir, 'db.faa'))
copy(join(self.datadir, 'DnaK', 'prot2tid.txt'),
join(self.tmpdir, 'taxon.map'))
me.build_blast_db()
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'))
remove(join(self.tmpdir, 'db.faa'))
remove(join(self.tmpdir, 'taxon.map'))
def test_build_blast_db(self):
me = Database()
me.output = self.tmpdir
me.makeblastdb = 'makeblastdb'
me.tmpdir = self.tmpdir
copy(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())
me.build_blast_db()
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'))
remove(join(self.tmpdir, 'db.faa'))
def test_genome_metadata(self):
me = Database()
me.output = self.tmpdir
me.df = pd.Series({
'genome':
'G1',
'accession':
'GCF_000123456.1',
'asm_name':
'ASM123v1',
'bioproject':
'PRJNA123456',
'biosample':
'SAMN00123456',
'assembly_level':
'Chromosome',
'organism_name':
'hypothetical organism',
'infraspecific_name':
'',
'isolate':
'',
'taxid':
'12345',
'ftp_path': ('ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/123/'
'456/GCF_000123456.1_ASM123v1'),
'proteins':
100,
'residues':
12500,
'whatever':
'nonsense'
}).to_frame().T
me.genome_metadata()
with open(join(self.tmpdir, 'genomes.tsv'), 'r') as f:
obs = f.read().splitlines()
exp = ('genome', 'proteins', 'residues', 'assembly_level', 'accession',
'bioproject', 'biosample', 'asm_name', 'organism_name',
'infraspecific_name', 'isolate', 'taxid', 'ftp_path')
self.assertEqual(obs[0], '\t'.join(exp))
exp = ('G1', '100', '12500', 'Chromosome', 'GCF_000123456.1',
'PRJNA123456', 'SAMN00123456', 'ASM123v1',
'hypothetical organism', '', '', '12345',
('ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/123/456/'
'GCF_000123456.1_ASM123v1'))
self.assertEqual(obs[1], '\t'.join(exp))
remove(join(self.tmpdir, 'genomes.tsv'))
def test_build_taxonmap(self):
me = Database()
me.output = self.tmpdir
me.taxdump = taxdump_from_text(taxdump_proteo)
me.p2tids = {
'P1': {'766'}, # Rickettsiales
'P2': {'570', '548'}, # Klebsiella
'P3': {'620', '622'}, # Shigella
'P4': {'561', '562'}, # Escherichia
'P5': {'126792', '28211'}
} # root
me.build_taxonmap()
exp = {'P1': '766', 'P2': '570', 'P3': '620', 'P4': '561', 'P5': '1'}
self.assertDictEqual(me.taxonmap, exp)
with gzip.open(join(self.tmpdir, 'taxon.map.gz'), 'rt') as f:
obs = dict(x.split('\t') for x in f.read().splitlines())
self.assertDictEqual(obs, exp)
remove(join(self.tmpdir, 'taxon.map.gz'))
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'))
def test_build_taxdump(self):
me = Database()
me.output = self.tmpdir
me.tmpdir = join(self.datadir, 'DnaK', 'taxdump')
me.taxdump = taxdump_from_text(taxdump_proteo)
data = (
('G1', '1224'), # Proteobacteria
('G2', '562'), # Escherichia coli
('G3', '585056'), # E. coli UMN026
('G4', '1038927')) # E. coli O104:H4
me.df = pd.DataFrame(data, columns=['genome',
'taxid']).set_index('genome')
me.build_taxdump()
with open(join(self.tmpdir, 'taxdump', 'nodes.dmp'), 'r') as f:
obs = set(x.split('\t')[0] for x in f.read().splitlines())
exp = {
'1', '131567', '2', '1224', '1236', '91347', '543', '561', '562',
'585056', '1038927'
}
self.assertSetEqual(obs, exp)
rmtree(join(self.tmpdir, 'taxdump'))