コード例 #1
0
 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()
コード例 #2
0
ファイル: QSetup.py プロジェクト: btownshend/pyTecan
 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()
コード例 #3
0
ファイル: MSetup.py プロジェクト: btownshend/pyTecan
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))
コード例 #4
0
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))
コード例 #5
0
ファイル: QSetup.py プロジェクト: qPCR4vir/pyTecan
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])
コード例 #6
0
ファイル: QSetup.py プロジェクト: qPCR4vir/pyTecan
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])