Python SeqGenUtils.writeFastaLinesToFile示例

示例#1

文件： compareCombinedModelAndInDomainModelKmers.py 项目： shwetabhandare/PySG

def writeFastaFileFromKmers(kmerList, prefix, outFileName):
	fastaFileLines = SeqGenUtils.createFastaFileFromKmers(kmerList, prefix);
	SeqGenUtils.writeFastaLinesToFile(fastaFileLines, outFileName);

示例#2

文件： kmerAnalysis.py 项目： shwetabhandare/PySG

	kmerDict = parseKspectrum.FindKspectrumKmers(featureFile, numKmers)
	HuR_ReString = '[^-](\d+\.\d+)\,HuR_([ATGC]+)'
	TTP_ReString = '[^-](\d+\.\d+)\,TTP_([ATGC]+)'

	HuRKmerDict = parseKspectrum.FindRBPSpecificKmers(featureFile, HuR_ReString, numKmers);
	TTPKmerDict = parseKspectrum.FindRBPSpecificKmers(featureFile, TTP_ReString, numKmers);


	kmerFastaLines = addFastaHeaderToKmers(kmerDict, "FeatureKmer")
	HuRFastaLines = addFastaHeaderToKmers(HuRKmerDict, "HuR_Specific")
	TTPFastaLines = addFastaHeaderToKmers(TTPKmerDict, "TTP_Specific")

	filename_prefix = os.path.splitext(sequenceFile)[0];
	filename_ext = os.path.splitext(sequenceFile)[1];
	HuR_Filename = filename_prefix + "_HuR" + filename_ext;
	TTP_Filename = filename_prefix + "_TTP" + filename_ext;

	SeqGenUtils.writeFastaLinesToFile(kmerFastaLines, sequenceFile)
	SeqGenUtils.writeFastaLinesToFile(HuRFastaLines, HuR_Filename)
	SeqGenUtils.writeFastaLinesToFile(TTPFastaLines, TTP_Filename)
	# topKmerFile = sys.argv[1]
	# signalType = sys.argv[2] ## PWM or PFM
	# signalFile = sys.argv[3]
	# seqFile = sys.argv[4]
	# topKmers = int(sys.argv[5])

	# kmerList = GetTopXKmers(topKmerFile, topKmers);
	# motif = GetMotifForSignal(signalType, signalFile);
	# seqDict  = SeqGenUtils.fasta_read(seqFile);
	# FindBestScoreSeqForMotif(motif, seqDict, kmerList)