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_filter_genomes(self):
me = Database()
header = ('# assembly_accession', 'assembly_level')
data = (('GCF_000000001.1', 'Chromosome'), ('GCF_000000002.1',
'Complete Genome'),
('GCF_000000003.2', 'Scaffold'), ('GCF_000000004.1', 'Contig'),
('GCA_000000004.1', 'Contig'))
df = pd.DataFrame(data, columns=header)
me.complete = False
me.genoids = None
me.exclude = False
# drop duplicates
me.df = df.copy()
me.filter_genomes()
self.assertEqual(me.df.shape[0], 4)
self.assertListEqual(
me.df['genome'].tolist(),
['G000000001', 'G000000002', 'G000000003', 'G000000004'])
self.assertEqual(
me.df.query('accession == "GCF_000000004.1"').shape[0], 1)
# complete genomes only
me.complete = True
me.df = df.copy()
me.filter_genomes()
self.assertListEqual(me.df['accnov'].tolist(),
['GCF_000000001', 'GCF_000000002'])
# include certain genomes
me.complete = False
me.genoids = 'G000000001,G000000003'
me.df = df.copy()
me.filter_genomes()
self.assertListEqual(me.df['accession'].tolist(),
['GCF_000000001.1', 'GCF_000000003.2'])
# exclude certain genomes
me.genoids = ['GCF_000000002.1', 'GCF_000000004']
me.exclude = True
me.df = df.copy()
me.filter_genomes()
self.assertListEqual(me.df['accession'].tolist(),
['GCF_000000001.1', 'GCF_000000003.2'])
def test_sample_by_taxonomy(self):
me = Database()
# do nothing
me.sample = None
self.assertIsNone(me.sample_by_taxonomy())
# xxx
header = ('genome', 'taxid', 'refseq_category', 'assembly_level')
data = (
('G1', '585056', '', 'Chromosome'), # E. coli UMN026
('G2', '1038927', 'representative genome', 'Chromosome'),
# E. coli O104:H4 (rep. genome to be prioritized over G1)
('G3', '2580236', '', 'Contig'), # sync E. coli
('G4', '622', '', 'Scaffold'), # Shigella
('G5', '548', '', 'Scaffold'), # Klebsiella
('G6', '126792', 'reference genome', 'Contig')) # plasmid
df = pd.DataFrame(data, columns=header)
me.reference = False
me.representative = False
me.taxdump = taxdump_from_text(taxdump_proteo)
# up to one genome per genus
me.rank = 'genus'
me.sample = 1
me.df = df.copy()
me.sample_by_taxonomy()
self.assertListEqual(me.df.columns.tolist(), list(header) + ['genus'])
self.assertListEqual(me.df['genome'].tolist(), ['G2', 'G4', 'G5'])
# include reference genome (plasmid)
me.reference = True
me.df = df.copy()
me.sample_by_taxonomy()
self.assertEqual(me.df['genome'].tolist()[-1], 'G6')
# up to two genomes for entire cellular life
me.rank = 'superkingdom'
me.sample = 2
me.reference = False
me.df = df.copy()
me.sample_by_taxonomy()
self.assertListEqual(me.df['genome'].tolist(), ['G1', 'G2'])
def test_identify_taxonomy(self):
me = Database()
header = ('organism_name', 'taxid', 'species', 'species_taxid')
data = (('Escherichia coli UMN026', '585056', 'E. coli', '562'),
('Escherichia coli O104:H4', '1038927', 'E. coli', '562'),
('Klebsiella aerogenes', '548', 'Klebsiella aerogenes',
'548'), ('unclassified Gammaproteobacteria', '118884', '',
''), ('Plasmid pPY113', '126792', '', ''))
df = pd.DataFrame(data, columns=header)
# organism names must be capital and latinate
me.capital = True
me.block = None
me.latin = True
me.taxids = None
me.exclude = False
me.taxdump = taxdump_from_text(taxdump_proteo)
me.df = df.copy()
me.identify_taxonomy()
self.assertNotIn('species_taxid', me.df.columns)
self.assertListEqual(me.df.index.tolist(), [0, 1, 2])
self.assertListEqual(me.df['species'].tolist(), ['562', '562', '548'])
# block word
me.block = 'plasmid'
me.latin = False
me.df = df.copy()
me.identify_taxonomy()
self.assertListEqual(me.df.index.tolist(), [0, 1, 2])
# no Escherichia
me.taxids = '561'
me.exclude = True
me.df = df.copy()
me.identify_taxonomy()
self.assertListEqual(me.df.index.tolist(), [2])
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_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'))
