def __init__(self,
trp,
vol=15,
maxdil=16,
mindilvol=90,
maxdilvol=100,
debug=False):
'Create a new QPCR setup structure'
self.volume = vol
self.samples = []
self.needDil = []
self.primers = []
self.nreplicates = []
self.dilProds = []
self.reuse = [
] # Index of prior dilution that can be used as input to this one; otherwise None
self.stages = []
self.MAXDIL = maxdil
self.MINDILVOL = mindilvol
self.MAXDILVOL = maxdilvol
self.trp = trp
self.debug = debug
self.dilutant = decklayout.SSDDIL
self.jobq = JobQueue()
self.e = Experiment()
def __init__(self,trp,vol=15,maxdil=16,mindilvol=50.0,maxdilvol=100.0,debug=False):
"""Create a new QPCR setup structure"""
self.volume=vol
self.samples=[]
self.needDil=[]
self.primers=[]
self.nreplicates=[]
self.dilProds=[]
self.reuse=[] # Index of prior dilution that can be used as input to this one; otherwise None
self.stages=[]
self.MAXDIL=maxdil
self.MINDILVOL=mindilvol
self.MAXDILVOL=maxdilvol
self.trp=trp
self.debug=debug
self.dilutant=decklayout.SSDDIL
self.jobq=JobQueue()
class MSetup(object):
TGTINVOL = 4
def __init__(self, trp, vol=15, maxdil=16, mindilvol=90, maxdilvol=100, debug=False):
"""Create a new QPCR setup structure"""
self.volume = vol
self.samples = []
self.needDil = []
self.primers = []
self.nreplicates = []
self.dilProds = []
self.reuse = [] # Index of prior dilution that can be used as input to this one; otherwise None
self.stages = []
self.MAXDIL = maxdil
self.MINDILVOL = mindilvol
self.MAXDILVOL = maxdilvol
self.trp = trp
self.debug = debug
self.dilutant = decklayout.SSDDIL
self.jobq = JobQueue()
self.e = Experiment()
def addSamples(self, src, needDil, primers, nreplicates=1, names=None, saveVol=None, saveDil=None, save=True):
"""Add sample(s) to list of qPCRs to do"""
# print "addSamples(%s)"%src
if not isinstance(src, list):
src = [src]
if save:
# saveVol is total amount (after dilution) to be immediately saved
if saveDil is None:
saveDil = min(needDil, self.MAXDIL)
if 1 < needDil / saveDil < 2:
saveDil = math.sqrt(needDil)
elif saveDil > needDil:
logging.warning("addSamples: saveDil=" + saveDil + ", but needDil is only " + needDil)
saveDil = needDil
if saveVol is None:
saveVol = max(self.MINDILVOL * 1.0 / saveDil, self.TGTINVOL)
if names is None:
tgt = [Sample(diluteName(src[i].name, saveDil), decklayout.DILPLATE) for i in range(len(src))]
else:
tgt = [Sample(diluteName(names[i], saveDil), decklayout.DILPLATE) for i in range(len(src))]
sv = tgt
for i in range(len(sv)):
# print "Save ",src[i]
svtmp = self.trp.runQPCRDIL(src=[src[i]], vol=saveVol * saveDil, srcdil=saveDil, tgt=[tgt[i]],
dilPlate=True, dilutant=self.dilutant)
sv[i] = svtmp[0]
else:
saveDil = 1
sv = src
needDil = needDil / saveDil
nstages = int(math.ceil(math.log(needDil) / math.log(self.MAXDIL)))
ndil = len(src) * (nstages + (1 if save else 0))
logging.notice("QPCR: %dQ/%dD [%s], dilution:%.1fx, primers: [%s]" % (
len(src) * len(primers) * nreplicates, ndil,
",".join([s.name for s in src]) if names is None else ",".join(names), needDil, ",".join(primers)))
for svi in range(len(sv)):
s = sv[svi]
if s.hasBeads:
prereqs = []
else:
j0 = self.jobq.addShake(sample=s, prereqs=[])
prereqs = [j0]
intermed = s
for i in range(nstages):
dil = math.pow(needDil, 1.0 / nstages)
# print "stage ",i,", needDil=",needDil,", dil=",dil
if i > 0:
vol = self.MAXDILVOL
else:
vol = min(self.MAXDILVOL * 1.0, max(self.MINDILVOL * 1.0, dil * self.TGTINVOL * 1.0))
if intermed.plate == decklayout.DILPLATE:
firstWell = intermed.well + 4 # Skip by 4 wells at a time to optimize multi-tip movements
else:
firstWell = 0
if not save and i == 0 and names is not None:
# Need to replace the name in this condition
dest = Sample(diluteName(names[svi], dil), decklayout.DILPLATE, firstWell=firstWell)
else:
dest = Sample(diluteName(intermed.name, dil), decklayout.DILPLATE, firstWell=firstWell)
# print "dest=",dest
j1 = self.jobq.addMultiTransfer(volume=vol * (dil - 1) / dil, src=self.dilutant, dest=dest, prereqs=[])
prereqs.append(j1)
j2 = self.jobq.addTransfer(volume=vol / dil, src=intermed, dest=dest, prereqs=prereqs)
# print "Dilution of %s was %.2f instead of %.2f (error=%.0f%%)"%(dest.name,(dil/(1+dil))/(1/dil),dil,((dil/(1+dil))/(1/dil)/dil-1)*100)
if dest.hasBeads:
prereqs = [j2]
else:
j3 = self.jobq.addShake(sample=dest, prereqs=[j2])
prereqs = [j3]
intermed = dest
self.dilProds = self.dilProds + [intermed]
self.primers = self.primers + [primers]
self.nreplicates = self.nreplicates + [nreplicates]
def allprimers(self):
return set([p for sublist in self.primers for p in sublist])
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 idler(self, t):
endTime = clock.elapsed() + t
if self.debug:
print("Idler(%.0f)" % t)
while clock.elapsed() < endTime:
j = self.jobq.getJob()
if j is None:
break
self.jobq.execJob(self.trp.e, j)
if self.debug:
print("Idler done with ", endTime - clock.elapsed(), " seconds remaining")
def run(self):
"""Run the dilutions and QPCR setup"""
# Setup qPCRs
# self.jobq.dump()
self.idler(100000)
self.trp.e.waitpgm() # May still need to wait for TC to complete before able to do final jobs
self.idler(100000)
if self.jobq.len() > 0:
logging.error("Blocked jobs remain on queue:")
self.jobq.dump()
assert False
tgt1 = Sample("Barcoded.Mixdown1", decklayout.EPPENDORFS)
for i in range(1, len(self.dilProds)):
self.e.transfer(12.5 * 1.2 * 2 / 1.5, self.dilProds[i], tgt1, mix=(False, False))
class MSetup(object):
TGTINVOL = 4
def __init__(self,
trp,
vol=15,
maxdil=16,
mindilvol=90,
maxdilvol=100,
debug=False):
'Create a new QPCR setup structure'
self.volume = vol
self.samples = []
self.needDil = []
self.primers = []
self.nreplicates = []
self.dilProds = []
self.reuse = [
] # Index of prior dilution that can be used as input to this one; otherwise None
self.stages = []
self.MAXDIL = maxdil
self.MINDILVOL = mindilvol
self.MAXDILVOL = maxdilvol
self.trp = trp
self.debug = debug
self.dilutant = decklayout.SSDDIL
self.jobq = JobQueue()
self.e = Experiment()
def addSamples(self,
src,
needDil,
primers,
nreplicates=1,
names=None,
saveVol=None,
saveDil=None,
save=True):
'Add sample(s) to list of qPCRs to do'
#print "addSamples(%s)"%src
if not isinstance(src, list):
src = [src]
if save:
# saveVol is total amount (after dilution) to be immediately saved
if saveDil is None:
saveDil = min(needDil, self.MAXDIL)
if needDil / saveDil > 1 and needDil / saveDil < 2:
saveDil = math.sqrt(needDil)
elif saveDil > needDil:
logging.warning("addSamples: saveDil=", saveDil,
", but needDil is only ", needDil)
saveDil = needDil
if saveVol is None:
saveVol = max(self.MINDILVOL * 1.0 / saveDil, self.TGTINVOL)
if names is None:
tgt = [
Sample(diluteName(src[i].name, saveDil),
decklayout.DILPLATE) for i in range(len(src))
]
else:
tgt = [
Sample(diluteName(names[i], saveDil), decklayout.DILPLATE)
for i in range(len(src))
]
sv = tgt
for i in range(len(sv)):
#print "Save ",src[i]
svtmp = self.trp.runQPCRDIL(src=[src[i]],
vol=saveVol * saveDil,
srcdil=saveDil,
tgt=[tgt[i]],
dilPlate=True,
dilutant=self.dilutant)
sv[i] = svtmp[0]
else:
saveDil = 1
sv = src
needDil = needDil / saveDil
nstages = int(math.ceil(math.log(needDil) / math.log(self.MAXDIL)))
ndil = len(src) * (nstages + (1 if save else 0))
logging.notice(
"QPCR: %dQ/%dD [%s], dilution:%.1fx, primers: [%s]" %
(len(src) * len(primers) * nreplicates, ndil,
",".join([s.name
for s in src]) if names is None else ",".join(names),
needDil, ",".join(primers)))
for svi in range(len(sv)):
s = sv[svi]
if s.hasBeads:
prereqs = []
else:
j0 = self.jobq.addShake(sample=s, prereqs=[])
prereqs = [j0]
intermed = s
for i in range(nstages):
dil = math.pow(needDil, 1.0 / nstages)
#print "stage ",i,", needDil=",needDil,", dil=",dil
if i > 0:
vol = self.MAXDILVOL
else:
vol = min(self.MAXDILVOL,
max(self.MINDILVOL, dil * self.TGTINVOL))
if intermed.plate == decklayout.DILPLATE:
firstWell = intermed.well + 4 # Skip by 4 wells at a time to optimize multi-tip movements
else:
firstWell = 0
if not save and i == 0 and names is not None:
# Need to replace the name in this condition
dest = Sample(diluteName(names[svi], dil),
decklayout.DILPLATE,
firstWell=firstWell)
else:
dest = Sample(diluteName(intermed.name, dil),
decklayout.DILPLATE,
firstWell=firstWell)
#print "dest=",dest
j1 = self.jobq.addMultiTransfer(volume=vol * (dil - 1) / dil,
src=self.dilutant,
dest=dest,
prereqs=[])
prereqs.append(j1)
j2 = self.jobq.addTransfer(volume=vol / dil,
src=intermed,
dest=dest,
prereqs=prereqs)
#print "Dilution of %s was %.2f instead of %.2f (error=%.0f%%)"%(dest.name,(dil/(1+dil))/(1/dil),dil,((dil/(1+dil))/(1/dil)/dil-1)*100)
if dest.hasBeads:
prereqs = [j2]
else:
j3 = self.jobq.addShake(sample=dest, prereqs=[j2])
prereqs = [j3]
intermed = dest
self.dilProds = self.dilProds + [intermed]
self.primers = self.primers + [primers]
self.nreplicates = self.nreplicates + [nreplicates]
def allprimers(self):
return set([p for sublist in self.primers for p in sublist])
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)
def idler(self, t):
endTime = clock.elapsed() + t
if self.debug:
print "Idler(%.0f)" % t
while clock.elapsed() < endTime:
j = self.jobq.getJob()
if j is None:
break
self.jobq.execJob(self.trp.e, j)
if self.debug:
print "Idler done with ", endTime - clock.elapsed(
), " seconds remaining"
def run(self):
'Run the dilutions and QPCR setup'
# Setup qPCRs
#self.jobq.dump()
self.idler(100000)
self.trp.e.waitpgm(
) # May still need to wait for PTC to complete before able to do final jobs
self.idler(100000)
if self.jobq.len() > 0:
logging.error("Blocked jobs remain on queue:", fatal=False)
self.jobq.dump()
assert False
tgt1 = Sample("Barcoded.Mixdown1", decklayout.EPPENDORFS)
for i in range(1, len(self.dilProds)):
self.e.transfer(12.5 * 1.2 * 2 / 1.5,
self.dilProds[i],
tgt1,
mix=(False, False))
class QSetup(object):
TGTINVOL = 4
def __init__(self,
trp,
vol=15,
maxdil=16,
mindilvol=50,
maxdilvol=100,
debug=False):
'Create a new QPCR setup structure'
self.volume = vol
self.samples = []
self.needDil = []
self.primers = []
self.nreplicates = []
self.dilProds = []
self.reuse = [
] # Index of prior dilution that can be used as input to this one; otherwise None
self.stages = []
self.MAXDIL = maxdil
self.MINDILVOL = mindilvol
self.MAXDILVOL = maxdilvol
self.trp = trp
self.debug = debug
self.dilutant = decklayout.SSDDIL
self.jobq = JobQueue()
def addSamples(self,
src,
needDil,
primers,
nreplicates=1,
names=None,
saveVol=None,
saveDil=None,
save=True):
'Add sample(s) to list of qPCRs to do'
#print "addSamples(%s)"%src
if not isinstance(src, list):
src = [src]
if save:
# saveVol is total amount (after dilution) to be immediately saved
if saveDil is None:
saveDil = min(needDil, self.MAXDIL)
if needDil / saveDil > 1 and needDil / saveDil < 2:
saveDil = math.sqrt(needDil)
elif saveDil > needDil:
print "addSamples: saveDil=", saveDil, ", but needDil is only ", needDil
saveDil = needDil
if saveVol is None:
saveVol = max(self.MINDILVOL * 1.0 / saveDil, self.TGTINVOL)
if names is None:
tgt = [
Sample(diluteName(src[i].name, saveDil),
decklayout.DILPLATE) for i in range(len(src))
]
else:
tgt = [
Sample(diluteName(names[i], saveDil), decklayout.DILPLATE)
for i in range(len(src))
]
sv = tgt
for i in range(len(sv)):
#print "Save ",src[i]
svtmp = self.trp.runQPCRDIL(src=[src[i]],
vol=saveVol * saveDil,
srcdil=saveDil,
tgt=[tgt[i]],
dilPlate=True,
dilutant=self.dilutant)
sv[i] = svtmp[0]
else:
saveDil = 1
sv = src
needDil = needDil / saveDil
nstages = int(math.ceil(math.log(needDil) / math.log(self.MAXDIL)))
for svi in range(len(sv)):
s = sv[svi]
if s.hasBeads:
prereqs = []
else:
j0 = self.jobq.addShake(sample=s, prereqs=[])
prereqs = [j0]
intermed = s
for i in range(nstages):
dil = math.pow(needDil, 1.0 / nstages)
#print "stage ",i,", needDil=",needDil,", dil=",dil
if i > 0:
vol = self.MAXDILVOL
else:
vol = min(self.MAXDILVOL,
max(self.MINDILVOL, dil * self.TGTINVOL))
if not save and i == 0 and names is not None:
# Need to replace the name in this condition
dest = Sample(diluteName(names[svi], dil),
decklayout.DILPLATE)
else:
dest = Sample(diluteName(intermed.name, dil),
decklayout.DILPLATE)
#print "dest=",dest
j1 = self.jobq.addMultiTransfer(volume=vol * (dil - 1) / dil,
src=self.dilutant,
dest=dest,
prereqs=[])
prereqs.append(j1)
j2 = self.jobq.addTransfer(volume=vol / dil,
src=intermed,
dest=dest,
prereqs=prereqs)
#print "Dilution of %s was %.2f instead of %.2f (error=%.0f%%)"%(dest.name,(dil/(1+dil))/(1/dil),dil,((dil/(1+dil))/(1/dil)/dil-1)*100)
if dest.hasBeads:
prereqs = [j2]
else:
j3 = self.jobq.addShake(sample=dest, prereqs=[j2])
prereqs = [j3]
intermed = dest
self.dilProds = self.dilProds + [intermed]
self.primers = self.primers + [primers]
self.nreplicates = self.nreplicates + [nreplicates]
def findReuses(self):
'Find any prior dilutions that can be reused'
maxstages = max(self.stages)
for j in range(len(self.samples)):
for i in range(len(self.samples)):
# Check if we can reuse i to form j
if i != j and self.samples[i] == self.samples[
j] and self.needDil[i] < self.needDil[
j] and self.needDil[i] > 1:
# Possible reuse
# Check if we already have a better one
if self.reuse[j] != None and self.needDil[
self.reuse[j]] > self.needDil[i]:
continue
# Check if it would increase number of stages
stages = int(
math.ceil(
math.log(self.needDil[j] / self.needDil[i]) /
math.log(self.MAXDIL)) + self.stages[i])
if stages > maxstages:
continue
print "Reuse %s@%f to form %s@%f" % (
self.samples[i], self.needDil[i], self.samples[j],
self.needDil[j])
self.reuse[j] = i
self.stages[j] = stages
totalDil = self.needDil[j]
stages = self.stages[j]
if self.reuse[j] != None:
totalDil = totalDil / self.needDil[self.reuse[j]]
stages = stages - self.stages[self.reuse[j]]
if stages > 1:
print "Need to form %s@%f by diluting %f in %d stages " % (
self.samples[j], self.needDil[j], totalDil, stages)
d = 1
if self.reuse[j] != None:
d = self.needDil[self.reuse[j]]
for k in range(stages - 1):
d = min(d * self.MAXDIL, totalDil)
self.addSamples(
[self.samples[j]], d,
[]) # Add extra intermediate that can be reused
if k == 0:
self.reuse[-1] = self.reuse[j]
else:
self.reuse[-1] = len(self.samples) - 2
self.reuse[j] = len(self.samples) - 1
for i in range(len(self.samples)):
print "%d: %s@%f" % (i, self.samples[i], self.needDil[i]),
if self.reuse[i] != None:
print ", use %d with additional %f dilution" % (
self.reuse[i],
self.needDil[i] / self.needDil[self.reuse[i]]),
print " [%d stages]" % self.stages[i]
def allprimers(self):
return set([p for sublist in self.primers for p in sublist])
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)
def idler(self, t):
endTime = clock.elapsed() + t
if self.debug:
print "Idler(%.0f)" % t
while clock.elapsed() < endTime:
j = self.jobq.getJob()
if j is None:
break
self.jobq.execJob(self.trp.e, j)
if self.debug:
print "Idler done with ", endTime - clock.elapsed(
), " seconds remaining"
def run(self):
'Run the dilutions and QPCR setup'
# Setup qPCRs
#self.jobq.dump()
self.idler(100000)
self.trp.e.waitpgm(
) # May still need to wait for PTC to complete before able to do final jobs
self.idler(100000)
if self.jobq.len() > 0:
print "Blocked jobs remain on queue:"
self.jobq.dump()
assert False
worklist.userprompt('Starting qPCR setup', timeout=5)
for p in self.allprimers():
# Build list of relevant entries
ind = [
i for i in range(len(self.dilProds)) if p in self.primers[i]
]
self.trp.runQPCR(src=[self.dilProds[i] for i in ind],
vol=self.volume,
srcdil=10.0 / 4,
primers=[p],
nreplicates=[self.nreplicates[i] for i in ind])
class QSetup(object):
TGTINVOL=4
def __init__(self,trp,vol=15,maxdil=16,mindilvol=50,maxdilvol=100,debug=False):
'Create a new QPCR setup structure'
self.volume=vol
self.samples=[]
self.needDil=[]
self.primers=[]
self.nreplicates=[]
self.dilProds=[]
self.reuse=[] # Index of prior dilution that can be used as input to this one; otherwise None
self.stages=[]
self.MAXDIL=maxdil
self.MINDILVOL=mindilvol
self.MAXDILVOL=maxdilvol
self.trp=trp
self.debug=debug
self.dilutant=decklayout.SSDDIL
self.jobq=JobQueue()
def addSamples(self, src, needDil, primers,nreplicates=1,names=None,saveVol=None,saveDil=None,save=True):
'Add sample(s) to list of qPCRs to do'
#print "addSamples(%s)"%src
if not isinstance(src,list):
src=[src]
if save:
# saveVol is total amount (after dilution) to be immediately saved
if saveDil is None:
saveDil=min(needDil,self.MAXDIL)
if needDil/saveDil>1 and needDil/saveDil<2:
saveDil=math.sqrt(needDil)
elif saveDil>needDil:
print "addSamples: saveDil=",saveDil, ", but needDil is only ", needDil
saveDil=needDil
if saveVol is None:
saveVol=max(self.MINDILVOL*1.0/saveDil,self.TGTINVOL)
if names is None:
tgt=[Sample(diluteName(src[i].name,saveDil),decklayout.DILPLATE) for i in range(len(src))]
else:
tgt=[Sample(diluteName(names[i],saveDil),decklayout.DILPLATE) for i in range(len(src))]
sv=tgt
for i in range(len(sv)):
#print "Save ",src[i]
svtmp=self.trp.runQPCRDIL(src=[src[i]],vol=saveVol*saveDil,srcdil=saveDil,tgt=[tgt[i]],dilPlate=True,dilutant=self.dilutant)
sv[i]=svtmp[0]
else:
saveDil=1
sv=src
needDil=needDil/saveDil
nstages=int(math.ceil(math.log(needDil)/math.log(self.MAXDIL)))
for svi in range(len(sv)):
s=sv[svi]
if s.hasBeads:
prereqs=[]
else:
j0=self.jobq.addShake(sample=s,prereqs=[])
prereqs=[j0]
intermed=s
for i in range(nstages):
dil=math.pow(needDil,1.0/nstages)
#print "stage ",i,", needDil=",needDil,", dil=",dil
if i>0:
vol=self.MAXDILVOL
else:
vol=min(self.MAXDILVOL,max(self.MINDILVOL,dil*self.TGTINVOL))
if not save and i==0 and names is not None:
# Need to replace the name in this condition
dest=Sample(diluteName(names[svi],dil),decklayout.DILPLATE)
else:
dest=Sample(diluteName(intermed.name,dil),decklayout.DILPLATE)
#print "dest=",dest
j1=self.jobq.addMultiTransfer(volume=vol*(dil-1)/dil,src=self.dilutant,dest=dest,prereqs=[])
prereqs.append(j1)
j2=self.jobq.addTransfer(volume=vol/dil,src=intermed,dest=dest,prereqs=prereqs)
#print "Dilution of %s was %.2f instead of %.2f (error=%.0f%%)"%(dest.name,(dil/(1+dil))/(1/dil),dil,((dil/(1+dil))/(1/dil)/dil-1)*100)
if dest.hasBeads:
prereqs=[j2]
else:
j3=self.jobq.addShake(sample=dest,prereqs=[j2])
prereqs=[j3]
intermed=dest
self.dilProds=self.dilProds+[intermed]
self.primers=self.primers+[primers]
self.nreplicates=self.nreplicates+[nreplicates]
def findReuses(self):
'Find any prior dilutions that can be reused'
maxstages=max(self.stages)
for j in range(len(self.samples)):
for i in range(len(self.samples)):
# Check if we can reuse i to form j
if i!=j and self.samples[i]==self.samples[j] and self.needDil[i]<self.needDil[j] and self.needDil[i]>1:
# Possible reuse
# Check if we already have a better one
if self.reuse[j]!=None and self.needDil[self.reuse[j]]>self.needDil[i]:
continue
# Check if it would increase number of stages
stages=int(math.ceil(math.log(self.needDil[j]/self.needDil[i])/math.log(self.MAXDIL))+self.stages[i])
if stages>maxstages:
continue
print "Reuse %s@%f to form %s@%f"%(self.samples[i],self.needDil[i],self.samples[j],self.needDil[j])
self.reuse[j]=i
self.stages[j]=stages
totalDil=self.needDil[j]
stages=self.stages[j]
if self.reuse[j] != None:
totalDil = totalDil / self.needDil[self.reuse[j]]
stages = stages - self.stages[self.reuse[j]]
if stages>1:
print "Need to form %s@%f by diluting %f in %d stages "%(self.samples[j],self.needDil[j],totalDil,stages)
d=1
if self.reuse[j]!=None:
d=self.needDil[self.reuse[j]]
for k in range(stages-1):
d=min(d*self.MAXDIL,totalDil)
self.addSamples([self.samples[j]],d,[]) # Add extra intermediate that can be reused
if k==0:
self.reuse[-1]=self.reuse[j]
else:
self.reuse[-1]=len(self.samples)-2
self.reuse[j]=len(self.samples)-1
for i in range(len(self.samples)):
print "%d: %s@%f"%(i,self.samples[i],self.needDil[i]),
if self.reuse[i]!=None:
print ", use %d with additional %f dilution"%(self.reuse[i], self.needDil[i]/self.needDil[self.reuse[i]]),
print " [%d stages]"%self.stages[i]
def allprimers(self):
return set([p for sublist in self.primers for p in sublist])
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)
def idler(self,t):
endTime=clock.elapsed()+t
if self.debug:
print "Idler(%.0f)"%t
while clock.elapsed()<endTime:
j=self.jobq.getJob()
if j is None:
break
self.jobq.execJob(self.trp.e,j)
if self.debug:
print "Idler done with ",endTime-clock.elapsed()," seconds remaining"
def run(self):
'Run the dilutions and QPCR setup'
# Setup qPCRs
#self.jobq.dump()
self.idler(100000)
self.trp.e.waitpgm() # May still need to wait for PTC to complete before able to do final jobs
self.idler(100000)
if self.jobq.len()>0:
print "Blocked jobs remain on queue:"
self.jobq.dump()
assert False
worklist.userprompt('Starting qPCR setup',timeout=5)
for p in self.allprimers():
# Build list of relevant entries
ind=[ i for i in range(len(self.dilProds)) if p in self.primers[i]]
self.trp.runQPCR(src=[self.dilProds[i] for i in ind],vol=self.volume,srcdil=10.0/4,primers=[p],nreplicates=[self.nreplicates[i] for i in ind])