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))