except KeyError:
print(
"Error: Augustus is not properly configured. Please review installation instructions"
)
sys.exit(1)
#get the possible species from augustus
augustus_list = []
for i in os.listdir(os.path.join(AUGUSTUS, 'species')):
if not i.startswith('.'):
augustus_list.append(i)
augustus_list = set(augustus_list)
d = flatten(natsorted(augustus_list))
print '--------------------------'
print 'AUGUSTUS species options:'
print '--------------------------'
print lib.list_columns(d, cols=3)
sys.exit(1)
elif sys.argv[1] == 'check':
arguments = sys.argv[2:]
cmd = os.path.join(script_path, 'util', 'check_modules.py')
arguments.insert(0, cmd)
exe = sys.executable
arguments.insert(0, exe)
subprocess.call(arguments)
sys.exit(1)
elif sys.argv[1] == 'setup':
help = """
Usage: funannotate %s <arguments>
version: %s
lib.SystemInfo()
#get version of funannotate
version = lib.get_version()
lib.log.info("Running %s" % version)
if args.outgroup:
if not os.path.isdir(os.path.join(parentdir, 'DB', 'outgroups')):
lib.log.error("Outgroup folder is not properly configured")
os._exit(1)
files = [f for f in os.listdir(os.path.join(parentdir, 'DB', 'outgroups'))]
files = [ x.replace('_buscos.fa', '') for x in files ]
files = [ x for x in files if not x.startswith('.') ]
if not args.outgroup in files:
lib.log.error("%s is not found in outgroups" % args.outgroup)
print lib.list_columns(natsorted(files), cols=3)
else:
outgroup = True
outgroup_species = os.path.join(parentdir, 'DB', 'outgroups', args.outgroup+'_buscos.fa')
outgroup_name = args.outgroup
else:
outgroup = False
outgroup_species = ''
outgroup_name = ''
#check dependencies and set path to proteinortho
if args.run_dnds:
programs = ['find_enrichment.py', 'mafft', 'raxmlHPC-PTHREADS', 'trimal', 'proteinortho5.pl', 'ete3', 'phyml']
else:
programs = ['find_enrichment.py', 'mafft', 'raxmlHPC-PTHREADS', 'trimal', 'proteinortho5.pl']