parentdir = os.path.dirname(currentdir)
sys.path.insert(0, parentdir)
import lib.library as lib
#get EVM arguments, genome, protein, transcript, min_intron, weights all from command line
cpus = int(sys.argv[2])
arguments = sys.argv[3:] #logfile first, num cpus is second
Output = arguments[-1]
del arguments[-1]
log_name = sys.argv[1]
if os.path.isfile(log_name):
os.remove(log_name)
#initialize script, log system info and cmd issue at runtime
lib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv) + '\n'
lib.log.debug(cmd_args)
#create output directory
tmpdir = 'EVM_tmp'
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
os.makedirs(tmpdir)
perl = 'perl'
EVM = os.environ['EVM_HOME']
Partition = os.path.join(EVM, 'EvmUtils', 'partition_EVM_inputs.pl')
Commands = os.path.join(EVM, 'EvmUtils', 'write_EVM_commands.pl')
Execute = os.path.join(EVM, 'EvmUtils', 'execute_EVM_commands.pl')
shutil.rmtree(go_folder)
os.makedirs(go_folder)
else:
os.makedirs(go_folder)
if not os.path.isdir(protortho):
os.makedirs(protortho)
if not os.path.isdir(phylogeny):
os.makedirs(phylogeny)
#create log file
log_name = os.path.join(args.out, 'funnannotate-compare.log')
if os.path.isfile(log_name):
os.remove(log_name)
#initialize script, log system info and cmd issue at runtime
lib.setupLogging(log_name)
FNULL = open(os.devnull, 'w')
cmd_args = " ".join(sys.argv)+'\n'
lib.log.debug(cmd_args)
print "-------------------------------------------------------"
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'))]
