else:
num = args.cpus
lib.log.debug("Running Augustus on %i chunks, using %i CPUs" %
(len(scaffolds), num))
lib.runMultiProgress(runAugustus, scaffolds, num)
lib.log.debug("Augustus prediction is finished, now concatenating results")
with open(os.path.join(tmpdir, 'augustus_all.gff3'), 'w') as output:
for file in scaffolds:
file = os.path.join(tmpdir, file + '.augustus.gff3')
with open(file) as input:
output.write(input.read())
if lib.checkannotations(os.path.join(tmpdir, 'augustus_all.gff3')):
lib.log.debug('Augustus finished, now joining results')
if lib.which_path('join_aug_pred.pl'):
join_script = 'join_aug_pred.pl'
else:
join_script = os.path.join(AUGUSTUS_BASE, 'scripts', 'join_aug_pred.pl')
cmd = '{:} < {:} > {:}'.format(join_script,
os.path.join(tmpdir, 'augustus_all.gff3'),
args.out)
lib.log.debug(cmd)
with open(args.out, 'w') as finalout:
with open(os.path.join(tmpdir, 'augustus_all.gff3'), 'r') as infile:
subprocess.call([join_script], stdin=infile, stdout=finalout)
if not args.debug:
shutil.rmtree(tmpdir)
ipr_properties = os.path.join(tmpdir, 'interproscan.properties')
downloadIPRproperties(ipr_properties, args.cpus_per_chunk)
if chunks > 1:
runMultiProgress(safe_run, file_list, threads, progress=args.progress)
else:
runDocker(file_list[0])
elif args.method == 'local':
if not args.iprscan_path:
print(
'You must specify location of interproscan.sh to --iprscan_path, exiting.'
)
sys.exit(1)
else:
if args.iprscan_path.endswith('interproscan.sh'):
iprpath = lib.which_path(args.iprscan_path)
else:
iprpath = os.path.join(args.iprscan_path, 'interproscan.sh')
if not os.path.isfile(iprpath):
print(('%s is not a valid path to interproscan.sh' % iprpath))
sys.exit(1)
print(
'Important: you need to manually configure your interproscan.properties file for embedded workers.'
)
print((
'Will try to launch %i interproscan processes, adjust -c,--cpus for your system'
% args.cpus))
if chunks > 1:
runMultiProgress(safe_run2,
file_list,
args.cpus,