def test_run(self):
dnaseSimulationFileName = "temp_dnaseSimulationFile.txt"
dnaseSimFh = fp.getFileHandle(dnaseSimulationFileName, 'w')
dnaseSimFh.write("sequenceName\tsequence\tmotifs\n")
dnaseSimFh.write(
"seq1\tACGTgaTATGATAGCACATGTCGTCAGTACCATGGTCGCCGCTTGCATAGGCAAACATAATTGG\tGATA4_HUMAN.H10MO.B-10,TAL1_known1-30,GATA4_HUMAN.H10MO.B-60\n"
)
dnaseSimFh.write(
"seq2\tACGTGAtaTGATAGCACATGTCGTCAGTACCATGGTCGCCGCTTGCATAGGCAAACATAATTGG\tGATA4_HUMAN.H10MO.B-5,TAL1_known1-35\n"
)
dnaseSimFh.write(
"seq3\tACGTGAtaTGATAGCACATGTCGTCAGTACCATGGTCGCCGCTTGCATAGGCAAACATAATTGG\t"
+ "GATA_disc1-5,GATA_known1-5,TAL1_known1-5," +
"GATA_disc1-55,GATA_known1-55,TAL1_known1-55\n"
) #last TAL1 won't get embedded
dnaseSimFh.write(
"seq4\tACGTGAtaTGATAGCACATGTCGTCAGTACCATGGTCGCCGCTTGCATAGGCAAACATAATTGG\t"
+ "GATA_disc1-30,GATA_known1-30,TAL1_known1-30,TAL1_known1-30\n")
dnaseSimFh.close()
dnaseSimulation = sn.DnaseSimulation(
dnaseSimulationFile=dnaseSimulationFileName,
loadedMotifs=sn.LoadedEncodeMotifs(
simdna.ENCODE_MOTIFS_PATH, pseudocountProb=0.001).addMotifs(
sn.LoadedHomerMotifs(simdna.HOCOMOCO_MOTIFS_PATH,
pseudocountProb=0.000)),
shuffler=sn.DinucleotideShuffler())
sn.printSequences("temp_dnaseSimulation.simdata",
dnaseSimulation,
includeFasta=False,
includeEmbeddings=True,
prefix=None)
def do(options):
outputFileName_core = util.addArguments("EmptyBackground", [
util.ArgumentToAdd(options.seqLength, "seqLength"),
util.ArgumentToAdd(options.numSeqs, "numSeqs")
])
embedInBackground = sn.EmbedInABackground(
backgroundGenerator=sn.ZeroOrderBackgroundGenerator(
seqLength=options.seqLength),
embedders=[])
sequenceSet = sn.GenerateSequenceNTimes(embedInBackground, options.numSeqs)
sn.printSequences(outputFileName_core + ".simdata",
sequenceSet,
includeFasta=True,
includeEmbeddings=True)
def do(options):
if (options.seed is not None):
import numpy as np
np.random.seed(options.seed)
import random
random.seed(options.seed)
outputFileName_core = util.addArguments("DensityEmbedding", [
util.ArgumentToAdd(options.prefix, "prefix"),
util.BooleanArgument(options.bestHit, "bestHit"),
util.ArrArgument(options.motifNames, "motifs"),
util.ArgumentToAdd(options.min_motifs, "min"),
util.ArgumentToAdd(options.max_motifs, "max"),
util.ArgumentToAdd(options.mean_motifs, "mean"),
util.FloatArgument(options.zero_prob, "zeroProb"),
util.ArgumentToAdd(options.seqLength, "seqLength"),
util.ArgumentToAdd(options.numSeqs, "numSeqs")
])
loadedMotifs = synthetic.LoadedEncodeMotifs(options.pathToMotifs,
pseudocountProb=0.001)
Constructor = synthetic.BestHitPwmFromLoadedMotifs if options.bestHit else synthetic.PwmSamplerFromLoadedMotifs
embedInBackground = synthetic.EmbedInABackground(
backgroundGenerator=synthetic.ZeroOrderBackgroundGenerator(
seqLength=options.seqLength),
embedders=[
synthetic.RepeatedEmbedder(
synthetic.SubstringEmbedder(
synthetic.ReverseComplementWrapper(
substringGenerator=Constructor(
loadedMotifs=loadedMotifs, motifName=motifName),
reverseComplementProb=options.rc_prob),
positionGenerator=synthetic.UniformPositionGenerator()),
quantityGenerator=synthetic.ZeroInflater(
synthetic.MinMaxWrapper(synthetic.PoissonQuantityGenerator(
options.mean_motifs),
theMax=options.max_motifs,
theMin=options.min_motifs),
zeroProb=options.zero_prob))
for motifName in options.motifNames
])
sequenceSet = synthetic.GenerateSequenceNTimes(embedInBackground,
options.numSeqs)
synthetic.printSequences(outputFileName_core + ".simdata",
sequenceSet,
includeFasta=True,
includeEmbeddings=True,
prefix=options.prefix)
def variableSpacingGrammar(options):
pc = 0.001
pathToMotifs = options.pathToMotifs
loadedMotifs = synthetic.LoadedEncodeMotifs(pathToMotifs, pseudocountProb=pc)
motifName1 = options.motifName1
motifName2 = options.motifName2
seqLength = options.seqLength
numSeq = options.numSeq
outputFileName = ("variableSpacingGrammarSimulation_"
+"prefix-"+options.prefix
+"_motif1-"+motifName1+"_motif2-"+motifName2
+"_seqLength"+str(seqLength)+"_numSeq"
+str(numSeq)+".simdata")
kwargs={'loadedMotifs':loadedMotifs}
theClass=synthetic.PwmSamplerFromLoadedMotifs
motif1Generator=theClass(motifName=motifName1,**kwargs)
motif2Generator=theClass(motifName=motifName2,**kwargs)
motif1Embedder=synthetic.SubstringEmbedder(substringGenerator=motif1Generator)
motif2Embedder=synthetic.SubstringEmbedder(substringGenerator=motif2Generator)
embedders = []
separationGenerator=synthetic.MinMaxWrapper(
synthetic.PoissonQuantityGenerator(options.meanSpacing),
theMin=options.minSpacing,
theMax=options.maxSpacing)
embedders.append(synthetic.EmbeddableEmbedder(
embeddableGenerator=synthetic.PairEmbeddableGenerator(
embeddableGenerator1=motif1Generator
,embeddableGenerator2=motif2Generator
,separationGenerator=separationGenerator
)
))
embedInBackground = synthetic.EmbedInABackground(
backgroundGenerator=synthetic.ZeroOrderBackgroundGenerator(seqLength)
, embedders=embedders
)
sequenceSet = synthetic.GenerateSequenceNTimes(embedInBackground, numSeq)
synthetic.printSequences(outputFileName, sequenceSet,
includeFasta=True, includeEmbeddings=True,
prefix=options.prefix)
def motifGrammarSimulation(options):
pc = 0.001
bestHit = options.bestHit
pathToMotifs = options.pathToMotifs
loadedMotifs = synthetic.LoadedEncodeMotifs(pathToMotifs,
pseudocountProb=pc)
motifName1 = options.motifName1
motifName2 = options.motifName2
seqLength = options.seqLength
numSeq = options.numSeq
generationSetting = options.generationSetting
outputFileName = "motifGrammarSimulation_" + generationSetting + (
"_bestHit" if bestHit else "")
if (generationSetting is not generationSettings.singleMotif2):
outputFileName += "_motif1-" + motifName1
if (generationSetting is not generationSettings.singleMotif1):
outputFileName += "_motif2-" + motifName2
outputFileName += "_seqLength" + str(seqLength) + "_numSeq" + str(
numSeq) + ".simdata"
kwargs = {'loadedMotifs': loadedMotifs}
if (bestHit):
theClass = synthetic.BestHitPwmFromLoadedMotifs
else:
theClass = synthetic.PwmSamplerFromLoadedMotifs
motif1Generator = theClass(motifName=motifName1, **kwargs)
motif2Generator = theClass(motifName=motifName2, **kwargs)
motif1Embedder = synthetic.SubstringEmbedder(
substringGenerator=motif1Generator)
motif2Embedder = synthetic.SubstringEmbedder(
substringGenerator=motif2Generator)
embedders = []
if (generationSetting == generationSettings.allBackground
or generationSetting == generationSettings.twoMotifs):
namePrefix = "synthNeg"
else:
namePrefix = "synthPos"
if (generationSetting == generationSettings.allBackground):
pass
elif (generationSetting in [
generationSettings.singleMotif1, generationSettings.twoMotifs,
generationSettings.singleMotif2
]):
if (generationSetting == generationSettings.singleMotif1):
embedders.append(motif1Embedder)
elif (generationSetting == generationSettings.singleMotif2):
embedders.append(motif2Embedder)
elif (generationSetting == generationSettings.twoMotifs):
embedders.append(motif1Embedder)
embedders.append(motif2Embedder)
else:
raise RuntimeError("Unsupported generation setting: " +
generationSetting)
elif (generationSetting in [
generationSettings.twoMotifsFixedSpacing,
generationSettings.twoMotifsVariableSpacing
]):
if (generationSetting == generationSettings.twoMotifsFixedSpacing):
separationGenerator = synthetic.FixedQuantityGenerator(
options.fixedSpacingOrMinSpacing)
elif (generationSetting == generationSettings.twoMotifsVariableSpacing
):
separationGenerator = synthetic.UniformIntegerGenerator(
minVal=options.fixedSpacingOrMinSpacing,
maxVal=options.maxSpacing)
else:
raise RuntimeError("unsupported generationSetting:" +
generationSetting)
embedders.append(
synthetic.EmbeddableEmbedder(
embeddableGenerator=synthetic.PairEmbeddableGenerator(
embeddableGenerator1=motif1Generator,
embeddableGenerator2=motif2Generator,
separationGenerator=separationGenerator)))
else:
raise RuntimeError("unsupported generationSetting:" +
generationSetting)
embedInBackground = synthetic.EmbedInABackground(
backgroundGenerator=synthetic.ZeroOrderBackgroundGenerator(seqLength),
embedders=embedders,
namePrefix=namePrefix)
sequenceSet = synthetic.GenerateSequenceNTimes(embedInBackground, numSeq)
synthetic.printSequences(outputFileName,
sequenceSet,
includeFasta=True,
includeEmbeddings=True)