def build_diamond_db(self):
"""Build DIAMOND database.
"""
# create temporary taxon map
taxonmap = join(self.tmpdir, 'prot.accession2taxid')
with open(taxonmap, 'w') as f:
f.write('accession\taccession.version\ttaxid\n')
for p, tid in sorted(self.taxonmap.items()):
f.write(f'{p.rsplit(".", 1)[0]}\t{p}\t{tid}\n')
# build DIAMOND database
makedirs(join(self.output, 'diamond'), exist_ok=True)
cmd = ' '.join(
(self.diamond, 'makedb', '--threads', str(self.threads), '--in',
join(self.output,
'db.faa'), '--taxonmap', taxonmap, '--taxonnodes',
join(self.output, 'taxdump', 'nodes.dmp'), '--taxonnames',
join(self.output, 'taxdump',
'names.dmp'), '--db', join(self.output, 'diamond',
'db'), '--tmpdir', self.tmpdir))
print('Build DIAMOND database...', flush=True)
ec, out = run_command(cmd)
if ec:
raise ValueError(f'diamond failed with error code {ec}.')
# clean up
remove(taxonmap)
print('Done.')
def test_run_command(self):
# simple command
cmd = 'echo "This is a test!"'
obs = run_command(cmd)
self.assertEqual(obs[0], 0)
self.assertListEqual(obs[1], ['This is a test!'])
# multiple-line output
cmd = 'for i in 1 2 3; do echo $i; done'
obs = run_command(cmd)[1]
self.assertListEqual(obs, ['1', '2', '3'])
# capture stderr
cmd = 'echo "This is an error!" >&2'
obs = run_command(cmd)[1]
self.assertListEqual(obs, ['This is an error!'])
def build_diamond_db(self):
"""Build DIAMOND database.
"""
# create temporary taxon map
taxonmap = join(self.tmpdir, 'prot.accession2taxid')
with open(taxonmap, 'w') as f:
f.write('accession\taccession.version\ttaxid\n')
for p, tid in sorted(self.taxonmap.items()):
f.write('{}\t{}\t{}\n'.format(p.rsplit('.', 1)[0], p, tid))
# build DIAMOND database
makedirs(join(self.output, 'diamond'), exist_ok=True)
cmd = ('{} makedb --threads {} --in {} --taxonmap {} --taxonnodes {} '
'--taxonnames {} --db {} --tmpdir {}'.format(
self.diamond, self.threads, join(self.output, 'db.faa'),
taxonmap, join(self.output, 'taxdump', 'nodes.dmp'),
join(self.output, 'taxdump', 'names.dmp'),
join(self.output, 'diamond', 'db'), self.tmpdir))
print('Build DIAMOND database...', flush=True)
ec, out = run_command(cmd, capture=False, merge=False)
if ec:
raise ValueError('diamond failed with error code {}.'.format(ec))
# clean up
remove(taxonmap)
print('Done.')
def build_blast_db(self):
"""Build BLAST database.
"""
makedirs(join(self.output, 'blast'), exist_ok=True)
cmd = ('{} -dbtype prot -in {} -out {} -title db -parse_seqids '
'-taxid_map {}'.format(self.makeblastdb,
join(self.output, 'db.faa'),
join(self.output, 'blast', 'db'),
join(self.output, 'taxon.map')))
print('Build BLAST database...', flush=True)
ec, out = run_command(cmd, capture=False)
if ec:
raise ValueError(
'makeblastdb failed with error code {}.'.format(ec))
print('Done.')
def build_blast_db(self):
"""Build BLAST database.
"""
makedirs(join(self.output, 'blast'), exist_ok=True)
cmd = ' '.join(
(self.makeblastdb, '-dbtype', 'prot', '-in',
join(self.output,
'db.faa'), '-out', join(self.output, 'blast',
'db'), '-title', 'db',
'-parse_seqids', '-taxid_map', join(self.output, 'taxon.map')))
print('Build BLAST database...', flush=True)
ec, out = run_command(cmd)
if ec:
raise ValueError(f'makeblastdb failed with error code {ec}.')
print('Done.')
def build_blast_db(self):
"""Build BLAST database.
"""
# create temporary taxon map
taxonmap = join(self.tmpdir, 'taxon.map')
with open(taxonmap, 'w') as f:
for p, tid in sorted(self.taxonmap.items()):
f.write(f'{p}\t{tid}\n')
# build BLAST database
makedirs(join(self.output, 'blast'), exist_ok=True)
cmd = ' '.join((self.makeblastdb, '-dbtype', 'prot', '-in',
join(self.output,
'db.faa'), '-out', join(self.output, 'blast',
'db'), '-title', 'db',
'-parse_seqids', '-taxid_map', taxonmap))
print('Build BLAST database...', flush=True)
ec, out = run_command(cmd)
if ec:
raise ValueError(f'makeblastdb failed with error code {ec}.')
# clean up
remove(taxonmap)
print('Done.')