def pwmoccsmethod(seqsdata, pwm, lambda_, Widx, numsamples, args):
logger.debug('Importance sampling using PWM importance weights')
calculateZn = jem.createZncalculatorFn(pwm, lambda_)
numpositive = numsamples / 2 # Sample half in each orientation
W = args.Ws[Widx]
childoccfreqs = jis.DistForFreqs(seqsdata.childoccfreqs[:, Widx])
cb = jis.importancesample(
seqsdata.index, W,
jis.WeightedSamplingDist(childoccfreqs, jis.PWMImportanceWeight(pwm)),
numpositive, jis.ISMemoCbAdaptor(W, jis.ZnSumCb(W), calculateZn))
return seqsdata.numoccs[Widx], jis.importancesample(
seqsdata.index, W,
jis.WeightedSamplingDist(childoccfreqs,
jis.PWMImportanceWeight(jem.pwmrevcomp(pwm))),
numsamples - numpositive, cb)
def pwmuniquemethod(seqsdata, pwm, lambda_, Widx, numsamples, args):
logger.debug('Importance sampling using PWM weights over unique W-mers')
calculateZn = jem.createZncalculatorFn(pwm, lambda_)
W = args.Ws[Widx]
childuniquefreqs = jis.DistForFreqs(seqsdata.childuniquefreqs[:, Widx])
childoccfreqs = jis.DistForFreqs(seqsdata.childoccfreqs[:, Widx])
numpositive = numsamples / 2 # Sample half in each orientation
cb = jis.importancesample(
seqsdata.index, W,
jis.WeightedSamplingDist(
childuniquefreqs,
jis.PWMImportanceWeightUnique(pwm, childoccfreqs)), numpositive,
jis.ISMemoCbAdaptor(W, jis.ZnSumCb(W), calculateZn, unique=True))
return seqsdata.numunique[Widx], jis.importancesample(
seqsdata.index, W,
jis.WeightedSamplingDist(
childuniquefreqs,
jis.PWMImportanceWeightUnique(jem.pwmrevcomp(pwm), childoccfreqs)),
numsamples - numpositive, cb)
def pwmoccsmethod(seqsdata, pwm, lambda_, Widx, numsamples, args):
logger.debug('Importance sampling using PWM importance weights')
calculateZn = jem.createZncalculatorFn(pwm, lambda_)
numpositive = numsamples / 2 # Sample half in each orientation
W = args.Ws[Widx]
childoccfreqs = jis.DistForFreqs(seqsdata.childoccfreqs[:, Widx])
cb = jis.importancesample(
seqsdata.index,
W,
jis.WeightedSamplingDist(
childoccfreqs,
jis.PWMImportanceWeight(pwm)),
numpositive,
jis.ISMemoCbAdaptor(W, jis.ZnSumCb(W), calculateZn))
return seqsdata.numoccs[Widx], jis.importancesample(
seqsdata.index,
W,
jis.WeightedSamplingDist(
childoccfreqs,
jis.PWMImportanceWeight(jem.pwmrevcomp(pwm))),
numsamples - numpositive,
cb)
def pwmuniquemethod(seqsdata, pwm, lambda_, Widx, numsamples, args):
logger.debug('Importance sampling using PWM weights over unique W-mers')
calculateZn = jem.createZncalculatorFn(pwm, lambda_)
W = args.Ws[Widx]
childuniquefreqs = jis.DistForFreqs(seqsdata.childuniquefreqs[:, Widx])
childoccfreqs = jis.DistForFreqs(seqsdata.childoccfreqs[:, Widx])
numpositive = numsamples / 2 # Sample half in each orientation
cb = jis.importancesample(
seqsdata.index,
W,
jis.WeightedSamplingDist(
childuniquefreqs,
jis.PWMImportanceWeightUnique(pwm, childoccfreqs)),
numpositive,
jis.ISMemoCbAdaptor(W, jis.ZnSumCb(W), calculateZn, unique=True))
return seqsdata.numunique[Widx], jis.importancesample(
seqsdata.index,
W,
jis.WeightedSamplingDist(
childuniquefreqs,
jis.PWMImportanceWeightUnique(jem.pwmrevcomp(pwm), childoccfreqs)),
numsamples - numpositive,
cb)