def convertIdsToTxIds(errorIds):
	"""read the sequence from a file in fasta format"""
	txList = list()
	for record in fasta.fasta_itr(three_utr_combined_file):
		header = record.header
		geneId, transcriptId, geneName = header.split('|')
		txList.append(transcriptId);

	for list1 in itertools.izip(errorIds):
		print list1
		for list2 in itertools.izip(list1[0]):
			idx = list2[0]
			print txList[idx]
	return txList;
    def constructFromFile(self, fileName, **args) :
        print 'reading from', fileName
        headerHandler = fastaHeaderHandler
        if 'headerHandler' in args :
            headerHandler = args['headerHandler']
        numPatterns = fasta.fasta_count(fileName)
        self.container.__init__(self, numPatterns)

        patternIDs = []
        L = []
        for record in fasta.fasta_itr(fileName) :
            self.addPattern(record.sequence)
            patternID, label = headerHandler(record.header)
            patternIDs.append(patternID)
            if label is not None :
                L.append(label)

        self.attachLabels(Labels(L, patternID = patternIDs, **args))
    def constructFromFile(self, fileName, **args):
        print 'reading from', fileName
        headerHandler = fastaHeaderHandler
        if 'headerHandler' in args:
            headerHandler = args['headerHandler']
        numPatterns = fasta.fasta_count(fileName)
        self.container.__init__(self, numPatterns)

        patternIDs = []
        L = []
        for record in fasta.fasta_itr(fileName):
            self.addPattern(record.sequence)
            patternID, label = headerHandler(record.header)
            patternIDs.append(patternID)
            if label is not None:
                L.append(label)

        self.attachLabels(Labels(L, patternID=patternIDs, **args))
def fasta_read(file_name) :
    """read the sequence from a file in fasta format"""
    return [record.sequence for record in fasta.fasta_itr(file_name)]
def fasta_read(file_name):
    """read the sequence from a file in fasta format"""
    return [record.sequence for record in fasta.fasta_itr(file_name)]