def runDiamond(input, query, cpus, output, premade_db=None):
# create DB of protein sequences
# check diamond version
if lib.getDiamondVersion() >= '2.0.5':
# run in frameshift mode
cmd = ['diamond', 'blastx', '--threads', str(cpus), '-q', input,
'--db', 'diamond', '-o', 'diamond.matches.tab', '-e', '1e-10',
'-k', '0', '--more-sensitive', '--unal', '0', '-c', '1', '-F', '15',
'-f', '6', 'sseqid', 'slen',
'sstart', 'send', 'qseqid', 'qlen', 'qstart', 'qend', 'pident',
'length', 'evalue', 'score', 'qcovhsp', 'qframe']
else:
if int(cpus) > 8:
cpus = 8
cmd = ['diamond', 'blastx', '--threads', str(cpus), '-q', input,
'--db', 'diamond', '-o', 'diamond.matches.tab', '-e', '1e-10',
'-k', '0', '--more-sensitive', '-f', '6', 'sseqid', 'slen',
'sstart', 'send', 'qseqid', 'qlen', 'qstart', 'qend', 'pident',
'length', 'evalue', 'score', 'qcovhsp', 'qframe']
if premade_db is None:
db_cmd = ['diamond', 'makedb', '--threads',
str(cpus), '--in', query, '--db', 'diamond']
lib.runSubprocess4(db_cmd, output, lib.log)
else:
lib.log.debug('Using premade Diamond database: {}'.format(premade_db))
os.symlink(os.path.abspath(premade_db),
os.path.join(output, 'diamond.dmnd'))
# now run search
lib.runSubprocess4(cmd, output, lib.log)
lib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv) + '\n'
lib.log.debug(cmd_args)
# get version of programs
exo_version = subprocess.Popen(
['exonerate', '--version'],
stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
exo_version = exo_version.split('version ')[-1]
blast_version = subprocess.Popen(
['tblastn', '-version'],
stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
blast_version = blast_version.split(': ')[-1]
if args.filter == 'diamond':
diamond_version = lib.getDiamondVersion()
def runDiamond(input, query, cpus, output):
# create DB of protein sequences
cmd = [
'diamond', 'makedb', '--threads',
str(cpus), '--in', query, '--db', 'diamond'
]
lib.runSubprocess4(cmd, output, lib.log)
# now run search
cmd = [
'diamond', 'blastx', '--threads',
str(cpus), '-q', input, '--db', 'diamond', '-o', 'diamond.matches.tab',
'-e', '1e-10', '-k', '0', '--more-sensitive', '-f', '6', 'sseqid',
'slen', 'sstart', 'send', 'qseqid', 'qlen', 'qstart', 'qend', 'pident',