def combineBlast(self, organismName, org_vs_UniprotBlastDB, Uniprot_vs_orgBlastDB): try: print "Combine Blast: " + organismName orgJointBlast = NGS_Util.createFilePath(self.orgBlastResDir, organismName + ".joint.blast") org_vs_UniprotBlastDB_fh = open(org_vs_UniprotBlastDB) Uniprot_vs_orgBlastDB_fh = open(Uniprot_vs_orgBlastDB) ec_files_fh = open(self.ec_files) orgJointBlast_fh = open(orgJointBlast, "w") combineBlasts(ec_files_fh, org_vs_UniprotBlastDB_fh, Uniprot_vs_orgBlastDB_fh, orgJointBlast_fh) org_vs_UniprotBlastDB_fh.close() Uniprot_vs_orgBlastDB_fh.close() ec_files_fh.close() orgJointBlast_fh.close() return orgJointBlast except Exception: print traceback.print_exc() return ""
#!/usr/bin/env python import sys, os from buildBlastResult import combineBlasts RESDIR = "blast_uniprot" f = open(sys.argv[1]) # org_list ecfn = sys.argv[2] # uniprot -> ec file names = list() for s in f: org, name = s.strip().split() names.append(name) for name in names: print "Processing %s..." % (name) bfn1 = "%s/%s-vs-up.blast" % (RESDIR, name) bfn2 = "%s/up-vs-%s.blast" % (RESDIR, name) bf1 = open(bfn1) bf2 = open(bfn2) ecf = open(ecfn) ofn = "%s/%s.joint.blast" % (RESDIR, name) of = open(ofn, "w") combineBlasts(ecf, bf1, bf2, of)