def reset(self):
'Reset this experiment so we can generate it again after adjusting the reagent initial volumes and total time'
totalTime=clock.elapsed()
clock.reset(totalTime)
#print "After reset, elapsed=%d"%clock.elapsed()
worklist.reset()
self.e=Experiment()
self.e.setreagenttemp(6.0)
self.e.sanitize(3,50) # Heavy sanitize
reagents.reset()
Sample.clearall()
decklayout.initWellKnownSamples()
def reset(self):
'Reset this experiment so we can generate it again after adjusting the reagent initial volumes and total time'
totalTime = clock.elapsed()
clock.reset(totalTime)
#print "After reset, elapsed=%d"%clock.elapsed()
worklist.reset()
self.e = Experiment()
self.e.setreagenttemp(6.0)
self.e.sanitize(3, 50) # Heavy sanitize
reagents.reset()
Sample.clearall()
decklayout.initWellKnownSamples()
def execute(self,ops):
reagents=None
for iteration in range(2):
print "Iteration ",iteration+1
# Need to clear here
trp=TRP()
if iteration==0:
trp.addTemplates(["IN"],200) # Add a template with stock concentration 200nM
else:
reagents=Sample.getAllOnPlate(Experiment.REAGENTPLATE)
for r in reagents:
if r.volume<0:
r.initvolume=-r.volume+10
Sample.clearall()
ops(self)
trp.finish()
reagents=None
for iteration in range(2):
print "Iteration ",iteration+1
trp=TRP()
if iteration==0:
trp.addTemplates(input,stockconc=10.0/6.0,units="x",plate=Experiment.EPPENDORFS) # Add a template
else:
reagents=Sample.getAllOnPlate(Experiment.REAGENTPLATE)+Sample.getAllOnPlate(Experiment.EPPENDORFS)
for r in reagents:
if r.volume<=0:
r.initvolume=-r.volume+r.plate.unusableVolume
Sample.clearall()
t71=trp.runT7(theo=False,src=srcs,tgt=[],vol=10,srcdil=10.0/6,dur=15,stopmaster=stop)
#print t71
t71=trp.diluteInPlace(tgt=t71,dil=5)
# Dilute input samples enough to use in qPCR directly (should be 5000/(rnagain*2*5) = 20)
qpcrdil1=trp.runQPCRDIL(src=t71,tgt=[],vol=100,srcdil=20,dilPlate=False)
rt1=trp.runRT(pos=True,src=t71,tgt=[],vol=30,srcdil=2)
rt1=trp.diluteInPlace(tgt=rt1,dil=5)
lig=trp.runLig(src=rt1*6,tgt=[],vol=20,srcdil=3,master=ligmaster1*3+ligmaster2*3)
prods=trp.diluteInPlace(tgt=lig,dil=10)
print "prod=",prods
for i in range(len(qpcrdil1)):
trp.runQPCR(src=qpcrdil1[i],vol=15,srcdil=10.0/4,primers=[tmplqpcr[i]],nreplicates=3)
input = "BT409"
srcprefix = "B"
prodprefix = "A"
for iteration in range(2):
print "Iteration ", iteration + 1
trp = TRP()
if iteration == 0:
trp.addTemplates([input],
200) # Add a template with stock concentration 200nM
else:
reagents = Sample.getAllOnPlate(Experiment.REAGENTPLATE)
for r in reagents:
if r.volume < 0:
r.initvolume = -r.volume + 20
Sample.clearall()
# Round 1 (Keep uncleaved +theo)
t71 = trp.runT7(theo=[False, True],
src=[input, input],
tgt=[],
vol=[16, 18],
srcdil=4)
sv1t7 = trp.saveSamps(src=t71, tgt=[], vol=10, dil=[4, 4])
rt1 = trp.runRT(pos=[True, True], src=t71, tgt=[], vol=[15, 22], srcdil=2)
trp.diluteInPlace(tgt=rt1, dil=2)
sv1rt = trp.saveSamps(src=rt1, tgt=[], vol=15, dil=2)
pcr1 = trp.runPCR(prefix=[srcprefix], src=rt1[1], tgt=[], vol=50, srcdil=4)
trp.diluteInPlace(tgt=pcr1, dil=3)
sv1pcr = trp.saveSamps(src=pcr1, tgt=["R1"], vol=125, dil=1)
