def InitDB(filename = None): """ By default, it will reuse the database already loaded-however, it will instantiate a new one, if there hasn't been one loaded so far. """ global biodb if biodb == None: biodb = biosettings.BioSettings(filename) biodb.InitDB() return biodb
pathway.AddGene(geneA) pathway.AddGene(geneB) pathway.Commit(self.biosettings) self.biosettings.RelatePathways(self.groupID, groupID, "PFAM", "") success = True else: if len(idsA) == 0: self.missingUni.add(uniA) else: self.ambiguousUni.add(uniA) if len(idsB) == 0: self.missingUni.add(uniB) else: self.ambiguousUni.add(uniB) else: print >> sys.stdout, "Misaligned Taxonomy (%s), %s %s : %s" % (name, taxA, taxB, comment) return success def Commit(self): self.biosettings.Commit() if __name__ == '__main__': filename = None if len(sys.argv) > 1: filename = sys.argv[1] bioDB = biosettings.BioSettings(filename) bioDB.OpenDB() loader = DIPLoader(bioDB) loader.Load() bioDB.Commit()
def LoadKB(dbFilename, kbLoads, doReset=False, refreshEnsembl=False): global loadables chromosomes = ('1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y', 'MT') bioDB = biosettings.BioSettings(dbFilename) bioDB.OpenDB() if doReset: bioDB.ResetDB() os.system("mkdir -p download") os.chdir("download") #variations = bioDB.BuildDbFilename(bioDB.filename, "var") ncbiLoader = ncbi_loader.NCBI_Loader(bioDB) if kbLoads[0] == "ALL": kbLoads = allgroups for kb in kbLoads: kb = kb.strip().lower() if kb == "snps": ncbiLoader.InitLog("snps.log") cwd = os.getcwd() ensembl = GetEnsembl(bioDB, refreshEnsembl) os.system("mkdir -p NCBI") os.chdir("NCBI") #ncbiLoader.UpdateSNPs(chromosomes, "variations", ensembl) os.chdir(cwd) ensembl.InitVariations("variations", chromosomes) ncbiLoader.CloseLog() elif kb == "genes": ncbiLoader.InitLog("genes.log") ensembl = GetEnsembl(bioDB, refreshEnsembl) #ensembl.ConnectToEnsemblDB(bioDB) ncbiLoader.UpdateGenes(ensembl, chromosomes) ncbiLoader.CloseLog() elif kb == "go": loader = load_go.GoLoader(bioDB) loader.InitLog() loader.Load() loader.CloseLog() elif kb == "kegg": loader = load_kegg.KeggLoader(bioDB) loader.InitLog() loader.Load() loader.CloseLog() elif kb == "reactome": loader = load_reactome.ReactomeLoader(bioDB) loader.InitLog() ensembl = GetEnsembl(bioDB, refreshEnsembl) loader.Load(ensembl) loader.Commit() bioDB.Commit() loader.CloseLog() elif kb == "netpath": loader = load_netpath.NetPathLoader(bioDB) loader.InitLog() loader.Load(False) loader.CloseLog() elif kb == "pfam": loader = load_pfam.PFamLoader(bioDB) loader.InitLog() loader.Load() bioDB.Commit() loader.CloseLog() elif kb == "dip": loader = load_dip.DIPLoader(bioDB) loader.InitLog() #loader.Load() #bioDB.Commit() loader.CloseLog() elif kb == "mint": loader = load_mint.MintLoader(bioDB) loader.InitLog() loader.Load() bioDB.Commit() loader.CloseLog() elif kb == "biogrid": loader = load_biogrid.BioGridLoader(bioDB) loader.InitLog() loader.Load() bioDB.Commit() loader.CloseLog() elif kb == "pharmgkb": print "Loading PharmGKB" loader = load_pharmgkb.PharmGKBLoader(bioDB) loader.InitLog() loader.Load() print "Attempting to Commit the data" loader.Commit() bioDB.Commit() loader.CloseLog() elif kb == "chainfiles": print "Loading Chain files" loader = load_chainfiles.ChainLoader(bioDB) loader.InitLog() loader.Load() loader.Commit() bioDB.Commit() loader.Commit() else: print >> sys.stderr, "Unknown kb name: %s. Options include: %s" % ( kb, ",".join(loadables))