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 ""
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)
#!/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)
