mode = int(sys.argv[1]) clusterUtil = MetabolicReconstructionPipeline_ClusterUtil.MetabolicReconstructionPipeline_ClusterUtil() clusterUtil.initialize(orgListFile, orgFastaDir, orgBlastResDir, jointBlastDir, orgGTGBlastResDir, GTGBestHitsDir, GTGKNNDir, orgIPRScanDir, InterProScan_EC_RAW_results, moveToDir) if mode == 0: pathToSeqs = NGS_Util.createFilePath(moveToDir, "data/org_sequence_db/") preProcess = MetabolicReconstructionPipeline_PreProcess.MetabolicReconstructionPipeline_PreProcess() preProcess.initialize(uniprot_fasta, uniprot_dust, uniprot_blast_db, nrdb40_fasta, nrdb40_dust, nrdb40_blast_db, orgListFile, orgFastaDir, seq_org_list, orgBlastDBDir, orgBlastDustDir, ec_files, uniprot_sprot_dat, keggAtomMapsDataDir ) preProcess.preProcess() successStat=True print("\nChecking input files that need to be downloaded ...............") successStat = successStat and NGS_Util.checkFile(uniprot_fasta) successStat = successStat and NGS_Util.checkFile(uniprot_sprot_dat) successStat = successStat and NGS_Util.checkFile(ec2go) print("\nChecking input files that need to be extracted for GTG ...............") successStat = successStat and NGS_Util.checkFile(nrdb40_fasta) successStat = successStat and NGS_Util.checkFile(nrdb40_dust) print("\n") if not successStat: raise Exception("Missing required input files") print("\nChecking Uniprot BLAST input...............") successStat = successStat and NGS_Util.checkFile(uniprot_blast_db + ".phd") successStat = successStat and NGS_Util.checkFile(uniprot_blast_db + ".psq") successStat = successStat and NGS_Util.checkFile(ec_files)