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)
