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'))]