def add_laplacian_correction(nbpos, nbneg, ngpos, ngneg, obpos, obneg, ogpos, ogneg):
#def add_laplacian_correction(nbpos, nbneg, obpos, obneg):
nbposn = int(LAPLACIAN_FRACTION * nbpos)
nbnegn = int(LAPLACIAN_FRACTION * nbneg)
ngposn = int(LAPLACIAN_FRACTION * nbpos)
ngnegn = int(LAPLACIAN_FRACTION * nbneg)
#print nposn, nnegn
# add points uniformly to both score ranges
for i in range(nbposn):
bnoise = (1.0 * i / (nbposn - 1)) * common.max_blast_joint_score()
obpos.write("%s\n" % (bnoise))
for i in range(nbnegn):
bnoise = (1.0 * i / (nbposn - 1)) * common.max_blast_joint_score()
obneg.write("%s\n" % (bnoise))
for i in range(ngposn):
gnoise = (1.0 * i / (ngposn - 1))
ogpos.write("%s\n" % (gnoise))
for i in range(ngnegn):
gnoise = (1.0 * i / (ngnegn - 1))
ogneg.write("%s\n" % (gnoise))
def plot(outfn,
orgname,
blastmin=0,
blastmax=common.max_blast_joint_score(),
format="png"):
if format == "png":
formats = ",width=1024,height=1024,pointsize=24"
else:
formats = ""
plotfn = "%s.R" % (outfn)
o = open(plotfn, "w")
o.write("""
bpos = read.table("%s.pos.blast")
bneg = read.table("%s.neg.blast")
gpos = read.table("%s.pos.gtg")
gneg = read.table("%s.neg.gtg")
blastpos = density(bpos[,1], from=%s, to=%s)
blastneg = density(bneg[,1], from=%s, to=%s)
gtgpos = density(gpos[,1], from=0, to=1)
gtgneg = density(gneg[,1], from=0, to=1)
name = c("BlastPos", "BlastNeg", "GTGPos", "GTGNeg")
bw = c(blastpos[3], blastneg[3], gtgpos[3], gtgneg[3])
write.table(cbind(blastpos$x, blastpos$y, blastpos$y / sum(blastpos$y)), file = "%s.blastpos")
write.table(cbind(blastneg$x, blastneg$y, blastneg$y / sum(blastneg$y)), file = "%s.blastneg")
write.table(cbind(gtgpos$x, gtgpos$y, gtgpos$y/sum(gtgpos$y)), file = "%s.gtgpos")
write.table(cbind(gtgneg$x, gtgneg$y, gtgneg$y/sum(gtgneg$y)), file = "%s.gtgneg")
write.csv(cbind(name, bw), file = "%s.bw")
%s(file = "%s-all.%s"%s)
par(mfrow=c(2,2), oma=c(2, 0, 3, 0), omi=c(0, 0, 0.8, 0))
blastpos$y = blastpos$y / sum(blastpos$y)
blastneg$y = blastneg$y / sum(blastneg$y)
gtgpos$y = gtgpos$y / sum(gtgpos$y)
gtgneg$y = gtgneg$y / sum(gtgneg$y)
plot(blastpos, main = "P(BLAST | r = 1)")
plot(blastneg, main = "P(BLAST | r = 0)")
plot(gtgpos, main = "P(GTG | r = 1)")
plot(gtgneg, main = "P(GTG | r = 0)")
dev.off()
""" % (outfn, outfn, outfn, outfn, blastmin, blastmax, blastmin, blastmax,
outfn, outfn, outfn, outfn, outfn, format, outfn, format, formats))
o.close()
subprocess.call("R CMD BATCH %s" % (plotfn), shell=True)
def add_laplacian_correction(nbpos, nbneg, ngpos, ngneg, obpos, obneg, ogpos,
ogneg):
#def add_laplacian_correction(nbpos, nbneg, obpos, obneg):
nbposn = int(LAPLACIAN_FRACTION * nbpos)
nbnegn = int(LAPLACIAN_FRACTION * nbneg)
ngposn = int(LAPLACIAN_FRACTION * nbpos)
ngnegn = int(LAPLACIAN_FRACTION * nbneg)
#print nposn, nnegn
# add points uniformly to both score ranges
for i in range(nbposn):
bnoise = (1.0 * i / (nbposn - 1)) * common.max_blast_joint_score()
obpos.write("%s\n" % (bnoise))
for i in range(nbnegn):
bnoise = (1.0 * i / (nbposn - 1)) * common.max_blast_joint_score()
obneg.write("%s\n" % (bnoise))
for i in range(ngposn):
gnoise = (1.0 * i / (ngposn - 1))
ogpos.write("%s\n" % (gnoise))
for i in range(ngnegn):
gnoise = (1.0 * i / (ngnegn - 1))
ogneg.write("%s\n" % (gnoise))
def plot(outfn, orgname, blastmin = 0, blastmax = common.max_blast_joint_score(), format = "png"):
if format == "png":
formats = ",width=1024,height=1024,pointsize=24"
else:
formats = ""
plotfn = "%s.R" % (outfn)
o = open(plotfn, "w")
o.write("""
bpos = read.table("%s.pos.blast")
bneg = read.table("%s.neg.blast")
gpos = read.table("%s.pos.gtg")
gneg = read.table("%s.neg.gtg")
blastpos = density(bpos[,1], from=%s, to=%s)
blastneg = density(bneg[,1], from=%s, to=%s)
gtgpos = density(gpos[,1], from=0, to=1)
gtgneg = density(gneg[,1], from=0, to=1)
name = c("BlastPos", "BlastNeg", "GTGPos", "GTGNeg")
bw = c(blastpos[3], blastneg[3], gtgpos[3], gtgneg[3])
write.table(cbind(blastpos$x, blastpos$y, blastpos$y / sum(blastpos$y)), file = "%s.blastpos")
write.table(cbind(blastneg$x, blastneg$y, blastneg$y / sum(blastneg$y)), file = "%s.blastneg")
write.table(cbind(gtgpos$x, gtgpos$y, gtgpos$y/sum(gtgpos$y)), file = "%s.gtgpos")
write.table(cbind(gtgneg$x, gtgneg$y, gtgneg$y/sum(gtgneg$y)), file = "%s.gtgneg")
write.csv(cbind(name, bw), file = "%s.bw")
%s(file = "%s-all.%s"%s)
par(mfrow=c(2,2), oma=c(2, 0, 3, 0), omi=c(0, 0, 0.8, 0))
blastpos$y = blastpos$y / sum(blastpos$y)
blastneg$y = blastneg$y / sum(blastneg$y)
gtgpos$y = gtgpos$y / sum(gtgpos$y)
gtgneg$y = gtgneg$y / sum(gtgneg$y)
plot(blastpos, main = "P(BLAST | r = 1)")
plot(blastneg, main = "P(BLAST | r = 0)")
plot(gtgpos, main = "P(GTG | r = 1)")
plot(gtgneg, main = "P(GTG | r = 0)")
dev.off()
""" % (outfn, outfn, outfn, outfn,
blastmin, blastmax, blastmin, blastmax,
outfn, outfn, outfn, outfn, outfn,
format, outfn, format, formats))
o.close()
subprocess.call("R CMD BATCH %s" % (plotfn), shell = True)
def estimate(ecscoresfn, modelecsfn, outfn, use_raw_scores = False):
f1 = open(ecscoresfn) # .ecscores/BLAST, GTG
f2 = open(modelecsfn) # list of EC numbers in model
orgname = modelecsfn[-4:]
modelecs = set()
for s in f2:
if s.startswith("#"):
continue
modelecs.add(s.strip())
#print modelecs
obpos = open("%s.pos.blast" % (outfn), "w")
obneg = open("%s.neg.blast" % (outfn), "w")
ogpos = open("%s.pos.gtg" % (outfn), "w")
ogneg = open("%s.neg.gtg" % (outfn), "w")
header = "#MaxScore\n"
obpos.write(header)
obneg.write(header)
ogpos.write(header)
ogneg.write(header)
nbpos = nbneg = ngpos = ngneg = 0
#nbpos = nbneg = 0
for line, s in enumerate(f1):
#print s.split("\t")
if s.startswith("#"):
continue
if use_raw_scores:
#EC BlastScore BlastQuerySeq BlastMatchSeq (.rawscore)
seq1, seq2, ecs, maxblast, maxgtg = s.strip().split("\t")
#ecs, jointp, seq1, seq2 = s.strip().split("\t")
#print seq1, seq2, ecs, jointp
else:
#.ecscore
#EC BlastScore BlastQuerySeq BlastMatchSeq GTGScore GTGQuerySeq GTGMatchSeq
#print s
ecs, maxblast, blastseq1, blastseq2, maxgtg, gtgseq1, gtgseq2 = s.strip().split("\t")
if ecs == "?" or not ec_pa.match(ecs):
continue
if ecs in modelecs:
if maxblast != "?":
obpos.write("%s\n" % (maxblast))
nbpos += 1
if maxgtg != "?":
ogpos.write("%s\n" % (maxgtg))
ngpos += 1
#print ecs
else:
if maxblast != "?":
obneg.write("%s\n" % (maxblast))
nbneg += 1
if maxgtg != "?":
ogneg.write("%s\n" % (maxgtg))
ngneg += 1
#print "%d pos, %d neg" % (npos, nneg)
add_laplacian_correction(nbpos, nbneg, ngpos, ngneg, obpos, obneg, ogpos, ogneg)
#add_laplacian_correction(nbpos, nbneg, obpos, obneg)
obpos.close()
obneg.close()
ogpos.close()
ogneg.close()
plot(outfn, orgname, 0, common.max_blast_joint_score(), "pdf")
plot(outfn, orgname, 0, common.max_blast_joint_score(), "png")
def estimate(ecscoresfn, modelecsfn, outfn, use_raw_scores=False):
f1 = open(ecscoresfn) # .ecscores/BLAST, GTG
f2 = open(modelecsfn) # list of EC numbers in model
orgname = modelecsfn[-4:]
modelecs = set()
for s in f2:
if s.startswith("#"):
continue
modelecs.add(s.strip())
#print modelecs
obpos = open("%s.pos.blast" % (outfn), "w")
obneg = open("%s.neg.blast" % (outfn), "w")
ogpos = open("%s.pos.gtg" % (outfn), "w")
ogneg = open("%s.neg.gtg" % (outfn), "w")
header = "#MaxScore\n"
obpos.write(header)
obneg.write(header)
ogpos.write(header)
ogneg.write(header)
nbpos = nbneg = ngpos = ngneg = 0
#nbpos = nbneg = 0
for line, s in enumerate(f1):
#print s.split("\t")
if s.startswith("#"):
continue
if use_raw_scores:
#EC BlastScore BlastQuerySeq BlastMatchSeq (.rawscore)
seq1, seq2, ecs, maxblast, maxgtg = s.strip().split("\t")
#ecs, jointp, seq1, seq2 = s.strip().split("\t")
#print seq1, seq2, ecs, jointp
else:
#.ecscore
#EC BlastScore BlastQuerySeq BlastMatchSeq GTGScore GTGQuerySeq GTGMatchSeq
ecs, maxblast, blastseq1, blastseq2, maxgtg, gtgseq1, gtgseq2 = s.strip(
).split("\t")
if ecs == "?" or not ec_pa.match(ecs):
continue
if ecs in modelecs:
if maxblast != "?":
obpos.write("%s\n" % (maxblast))
nbpos += 1
if maxgtg != "?":
ogpos.write("%s\n" % (maxgtg))
ngpos += 1
#print ecs
else:
if maxblast != "?":
obneg.write("%s\n" % (maxblast))
nbneg += 1
if maxgtg != "?":
ogneg.write("%s\n" % (maxgtg))
ngneg += 1
#print "%d pos, %d neg" % (npos, nneg)
add_laplacian_correction(nbpos, nbneg, ngpos, ngneg, obpos, obneg, ogpos,
ogneg)
#add_laplacian_correction(nbpos, nbneg, obpos, obneg)
obpos.close()
obneg.close()
ogpos.close()
ogneg.close()
plot(outfn, orgname, 0, common.max_blast_joint_score(), "pdf")
plot(outfn, orgname, 0, common.max_blast_joint_score(), "png")
