def addReferences(self, mindil=1, nsteps=6, dstep=4, nreplicates=1, ref=None, primers=None):
"""Add all needed references"""
# print "addReferences(mindil=",mindil,", nsteps=",nsteps,", dstep=",dstep,", nrep=", nreplicates, ", ref=",ref,")"
# Make sure the ref reagent is loaded
if ref is None:
ref = reagents.getsample("QPCRREF")
if primers is None:
primers = self.allprimers()
dils = [1.0]
for i in range(nsteps):
needDil = mindil * math.pow(dstep, i)
srcDil = 1
src = [ref]
for j in range(len(dils)):
if needDil / dils[j] <= self.MAXDIL:
srcDil = dils[j]
if srcDil == 1:
src = [ref]
else:
srcname = "%s.D%d" % (ref.name, srcDil)
src = [Sample.lookup(srcname)]
if src[0] is None:
src = [Sample(srcname, decklayout.DILPLATE)]
break
tmp = self.MINDILVOL
self.MINDILVOL = 75 # Make sure there's enough for resuing dilutions
self.addSamples(src=src, needDil=needDil / srcDil, primers=primers, nreplicates=nreplicates,
save=needDil / srcDil > self.MAXDIL, saveVol=75)
self.MINDILVOL = tmp
dils.append(needDil)
self.addSamples(src=[self.dilutant], needDil=1, primers=primers, nreplicates=nreplicates, save=False)
def addReferences(self,mindil=1,nsteps=6,dstep=4,nreplicates=1,ref=None,primers=None):
'Add all needed references'
#print "addReferences(mindil=",mindil,", nsteps=",nsteps,", dstep=",dstep,", nrep=", nreplicates, ", ref=",ref,")"
# Make sure the ref reagent is loaded
if ref is None:
ref=reagents.getsample("QPCRREF")
if primers is None:
primers=self.allprimers()
dils=[1]
for i in range(nsteps):
needDil=mindil*math.pow(dstep,i)
srcDil=1
src=[ref]
for j in range(len(dils)):
if needDil/dils[j] <= self.MAXDIL:
srcDil=dils[j]
if srcDil==1:
src=[ref]
else:
srcname="%s.D%d"%(ref.name,srcDil)
src=[Sample.lookup(srcname)]
if src[0] is None:
src=[Sample(srcname,decklayout.DILPLATE)]
break
tmp=self.MINDILVOL
self.MINDILVOL=75 # Make sure there's enough for resuing dilutions
self.addSamples(src=src,needDil=needDil/srcDil,primers=primers,nreplicates=nreplicates,save=needDil/srcDil>self.MAXDIL,saveVol=75)
self.MINDILVOL=tmp
dils.append(needDil)
self.addSamples(src=[self.dilutant],needDil=1,primers=primers,nreplicates=nreplicates,save=False)
tmplqpcr=tmplqpcr+[srcprefix[i]+srcsuffix[i]]
ligmaster1=ligmaster1+["MLig"+ligprefix1[i]+stem1[i]]
pcr1=pcr1+[(srcprefix[i]+srcsuffix[i],ligprefix1[i]+srcsuffix[i])]
ligmaster2=ligmaster2+["MLig"+ligprefix2[i]+stem1[i]]
pcr2=pcr2+[(srcprefix[i]+srcsuffix[i],ligprefix2[i]+srcsuffix[i])]
print "srcs=",srcs
print "tmplqpcr=",tmplqpcr
print "ligmaster1=",ligmaster1
print "pcr1=",pcr1
print "ligmaster2=",ligmaster2
print "pcr2=",pcr2
# Create ligation master mix samples
for lm in set(ligmaster1+ligmaster2):
if Sample.lookup(lm)==None:
Sample(lm,Experiment.REAGENTPLATE,None,3)
for st in set(stop):
if Sample.lookup(st)==None:
Sample(st,Experiment.REAGENTPLATE,None,2)
for p in pcr1+pcr2:
for pm in p:
if Sample.lookup("MQ"+pm)==None:
Sample("MQ"+pm,Experiment.REAGENTPLATE,None,10.0/6)
for pm in tmplqpcr:
if Sample.lookup("MQ"+pm)==None:
Sample("MQ"+pm,Experiment.REAGENTPLATE,None,10.0/6)
srcs = srcs + [input[i]]
tmplqpcr = tmplqpcr + [srcprefix[i] + srcsuffix[i]]
ligmaster = ligmaster + ["MLig" + ligprefix[i] + stem1[i]]
pcr = pcr + [
(srcprefix[i] + srcsuffix[i], ligprefix[i] + srcsuffix[i])
]
stop = stop + ["MStp" + srcsuffix[i]]
#print srcs
#print tmplqpcr
#print ligmaster
#print pcr
# Create ligation master mix samples
for lm in set(ligmaster):
if Sample.lookup(lm) == None:
Sample(lm, Experiment.REAGENTPLATE, None, 3)
for st in set(stop):
if Sample.lookup(st) == None:
Sample(st, Experiment.REAGENTPLATE, None, 2)
for p in pcr:
for pm in p:
if Sample.lookup("MQ" + pm) == None:
Sample("MQ" + pm, Experiment.REAGENTPLATE, None, 10.0 / 6)
for pm in tmplqpcr:
if Sample.lookup("MQ" + pm) == None:
Sample("MQ" + pm, Experiment.REAGENTPLATE, None, 10.0 / 6)
srcs = []
for k in range(max(nreplicates)):
for i in range(len(input)):
if nreplicates[i] > k:
srcs = srcs + [input[i]]
tmplqpcr = [srcprefix + srcsuffix]
pcr = [srcprefix + srcsuffix, ligprefix + srcsuffix]
print "srcs=", srcs
print "tmplqpcr=", tmplqpcr
print "ligmaster=", ligmaster
print "pcr=", pcr
print "stop=", stop
# Create ligation master mix samples
if Sample.lookup(ligmaster) == None:
Sample(ligmaster, Experiment.REAGENTPLATE, None, 3)
if Sample.lookup(stop) == None:
Sample(stop, Experiment.REAGENTPLATE, None, 2)
for pm in pcr:
if Sample.lookup("MQ" + pm) == None:
Sample("MQ" + pm, Experiment.REAGENTPLATE, None, 10.0 / 6)
for pm in tmplqpcr:
if Sample.lookup("MQ" + pm) == None:
Sample("MQ" + pm, Experiment.REAGENTPLATE, None, 10.0 / 6)
reagents = None
srcs=[]
for k in range(max(nreplicates)):
for i in range(len(input)):
if nreplicates[i]>k:
srcs=srcs+[input[i]]
tmplqpcr=[srcprefix+srcsuffix]
pcr=[srcprefix+srcsuffix,ligprefix+srcsuffix]
print "srcs=",srcs
print "tmplqpcr=",tmplqpcr
print "ligmaster=",ligmaster
print "pcr=",pcr
print "stop=",stop
# Create ligation master mix samples
if Sample.lookup(ligmaster)==None:
Sample(ligmaster,Experiment.REAGENTPLATE,None,3)
if Sample.lookup(stop)==None:
Sample(stop,Experiment.REAGENTPLATE,None,2)
for pm in pcr:
if Sample.lookup("MQ"+pm)==None:
Sample("MQ"+pm,Experiment.REAGENTPLATE,None,10.0/6)
for pm in tmplqpcr:
if Sample.lookup("MQ"+pm)==None:
Sample("MQ"+pm,Experiment.REAGENTPLATE,None,10.0/6)
reagents=None
