Python getPSSMListFromDremeFile示例

示例#1

文件： test_compare_kmers.py 项目： shwetabhandare/PySG

	def test_getKmerREFromPSSM(self):
		predictedDremeFile = "/projects/bhandare/workspace/PySG/src/resources/dreme.txt"
		seq = "CTGTCCCTTTTCGGGTTTTTTTTTTCCGAGCGGCCTCGGTGGGTGAAATGAACGACACTCATGCGAGCGACACTAGGGCGCCGTTCGTTCTGTGCACCCA"
		pssmList = parseDreme.getPSSMListFromDremeFile(predictedDremeFile);
		kmerREString = compareKmerCommon.getKmerFromPSSM(pssmList, seq)

		self.assertEqual(kmerREString, '(TCGGGT|TTTTTT)')

示例#2

文件： dremeSequenceBasedComparison.py 项目： shwetabhandare/PySG

def computeSequenceBasedDREMEResults(dremeFile, realCsvFile, posSeqFile, negSeqFile):
	totalPosTP = totalPosFP = totalPosFN = totalPosTN = 0;
	totalNegTP = totalNegFP = totalNegFN = totalNegTN = 0;

	posSeqDict  = SeqGenUtils.fasta_read(posSeqFile);
	negSeqDict  = SeqGenUtils.fasta_read(negSeqFile);
	realKmerDict = parseRealKmers.GetRealKmerDict(realCsvFile);
	pssmList = parseDreme.getPSSMListFromDremeFile(dremeFile)

	numPosTP, numPosFP, numPosFN, numPosTN = compareRealAndPredicted(realKmerDict, posSeqDict, pssmList, positive=True)
	numNegTP, numNegFP, numNegFN, numNegTN = compareRealAndPredicted(realKmerDict, negSeqDict, pssmList, False)

	print "Positive: TP: ", numPosTP, ", FP: ", numPosFP, ", FN: ", numPosFN, ", TN: ", numPosTN
	print "Negative: TP: ", numNegTP, ", FP: ", numNegFP, ", FN: ", numNegFN, ", TN: ", numNegTN

	totalPos = len(posSeqDict)
	totalNeg = len(negSeqDict)

	sensitivity, ppv = compareKmers.GetSensitivityAndPPV((numPosTP + numNegTP) , (numPosFP + numNegFP), (numPosFN + numNegFN))
	accuracy = compareKmers.GetAccuracy( (numPosTP + numNegTP), (numPosTN + numNegTN),  (totalPos + totalNeg) )
	specificity = compareKmers.GetSpecificity( (numPosFP + numNegFP), totalNeg);

	print "Senitivity: ", sensitivity, ", PPV: ", ppv, ", Accuracy: ", accuracy, ", Specificity: ", specificity;
	return sensitivity, ppv;	

示例#3

文件： compareKmers.py 项目： shwetabhandare/PySG

def GetDremePSSM(predictedDremeFile):
	pssmList = parseDreme.getPSSMListFromDremeFile(predictedDremeFile);
	return pssmList;

示例#4

文件： TAMO_Motif.py 项目： shwetabhandare/PySG

	#print "Motif:", motif.source
	#print "Max Motif Score:", motif.maxscore
	#print "Motif Summary:", motif.summary()
	#motif.printlogo(2.3,10)
	
	return motif
#end Make_PWM_Motif

##########################################################################################

def Make_Text_Motif(textMotif):
	return MotifTools.Motif_from_text(textMotif)

if __name__ == "__main__":
	dremeFile = sys.argv[1]
	pssmList = parseDreme.getPSSMListFromDremeFile(dremeFile);
	for pssmLines in pssmList:
		Read_Dreme_PSSM(pssmLines);

if __name__ == "__main__":
	import sys
	pwmFile = sys.argv[1]
	type = sys.argv[2]
	if type == "pwm":
		motif = Make_PWM_Motif(pwmFile)
	elif type == "pfm":
		motif = Make_PFM_Motif(pwmFile)
	print motif;