def __init__(self, inFile): # print inFile self.isSeql = False self.charEncoding = 'not known' try: with open(inFile, 'r') as f: self.charEncoding = chardet.detect(f.read())['encoding'] self.seqlGenerator = su.generateChunks(inFile, pa) generalInformationString = self.seqlGenerator.next()['chunk'] generalInformationUnicode = generalInformationString.decode(self.charEncoding) # self.generalInformation = GeneralInformation(generalInformationString) self.generalInformation = GeneralInformation(generalInformationUnicode) if self.generalInformation.genInfoPatternFound: self.isSeql = True # print 'SequenceListing initialised for file', inFile except IOError: # self.logger.exception("Invalid input file: %s" % self.in_file_name) print 'Invalid file name', inFile self.quantity_nuc = 0 self.quantity_prt = 0 self.quantity_mix = 0
def __init__(self, inFile): # print inFile self.isSeql = False try: self.seqlGenerator = su.generateChunks(inFile, pa) generalInformationString = self.seqlGenerator.next()['chunk'] self.generalInformation = GeneralInformation(generalInformationString) if self.generalInformation.genInfoPatternFound: self.isSeql = True # print 'SequenceListing initialised for file', inFile except IOError: # self.logger.exception("Invalid input file: %s" % self.in_file_name) print 'Invalid file name', inFile
def getSequenceFromFile(cls, aFile, aSeqIdNo): ''' Return the Sequence instance corresponding to aSeqIdNo in aFile. The assumption is that seqIdNo = actualSeqIdNo. :param aFile: a sequence listing file :param aSeqIdNo: int representing the seq id no :return: Sequence ''' # TODO: test it listOfChunks = [] for c in su.generateChunks(aFile, pa): listOfChunks.append(c) inputString = listOfChunks[aSeqIdNo]['chunk'] seq = Sequence(inputString) seq.actualSeqIdNo = aSeqIdNo#TODO: to see if this is OK return seq
def getSequenceFromFile(cls, aFile, aSeqIdNo): ''' Return the Sequence instance corresponding to aSeqIdNo in aFile. The assumption is that seqIdNo = actualSeqIdNo. :param aFile: a sequence listing file :param aSeqIdNo: int representing the seq id no :return: Sequence ''' # TODO: test it, unicode it! listOfChunks = [] for c in su.generateChunks(aFile, pa): listOfChunks.append(c) inputString = listOfChunks[aSeqIdNo]['chunk'] seq = Sequence(inputString) seq.actualSeqIdNo = aSeqIdNo#TODO: to see if this is OK return seq