def __init__( self, delimiter='\t', comment='#' ): FlatFileParser.__init__( self, delimiter, comment ) requiredHeaders = {"bNumber":"Name", "gene":"gene", "function":"function"} optionalHeaders = {} self.addRequiredHeaders( requiredHeaders ) self.addOptionalHeaders( optionalHeaders )
def __init__( self, delimiter='\t', comment='#' ): FlatFileParser.__init__( self, delimiter, comment ) requiredHeaders = {"Abbreviation":"Name", "OfficialName":"OfficialName", "Equation":"Equation"} optionalHeaders = {} self.addRequiredHeaders( requiredHeaders ) self.addOptionalHeaders( optionalHeaders )
def __init__( self, delimiter='\t',comment="#"): FlatFileParser.__init__( self, delimiter, comment ) requiredHeaders = {"Flux":"Name", "Coefficient":"Coefficient"} optionalHeaders = {} self.addRequiredHeaders( requiredHeaders ) self.addOptionalHeaders( optionalHeaders )
def __init__(self,delimiter='\t',comment='#'): FlatFileParser.__init__( self, delimiter, comment ) requiredHeaders = {"Abbreviation":"Name", "OfficialName":"OfficialName"} optionalHeaders = {"concentration":"concentration","lower":"lower","upper":"upper","compartment":"compartment"} self.addRequiredHeaders( requiredHeaders ) self.addOptionalHeaders( optionalHeaders )
def parseAnnotationFiles(self,annotationFiles): parser = FlatFileParser() result = {} for (name,keyTag,fileName) in annotationFiles: annotation = parser.parseGenericReport(fileName, keyTag, unique=True) result[name] = annotation return result
def __init__( self, delimiter='\t', comment='#' ): FlatFileParser.__init__( self, delimiter, comment ) self.reactionParser = ReactionParser() requiredHeaders = { "Abbreviation":"name", "Equation":"equation", "Lower Bound":"lowerBound", "Upper Bound":"upperBound" } optionalHeaders = {"objective":"objective"} self.addRequiredHeaders( requiredHeaders ) self.addOptionalHeaders( optionalHeaders ) self.setObjectiveTag( "objective function" )
def __init__( self, delimiter='\t', comment='#' ): FlatFileParser.__init__( self, delimiter, comment ) self.setHeader( ["Flux", "Coefficient"] )
def __init__( self, delimiter='\t', comment='#' ): FlatFileParser.__init__( self, delimiter, comment ) self.setHeader( ["Flux", "Lower", "Upper"] ) self.noLimit = ['None'] self.posInf = 1e3 self.negInf = -1e3
parser = OptionParser() parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default=False, help="set verbose mode") parser.add_option("-f", "--file", dest="input_file", default=None, help="test input file") parser.add_option("-o", "--output", dest="output_file", default=None, help="test output file") (options,args) = parser.parse_args() input_file = options.input_file output_file = options.output_file input_file = 'Variance__Report.txt' input_file = 'Variance_FC_00707_Report.txt' output_file = 'Original_Report_out_test.txt' print "Reading report file [%s]" %(input_file) s_read_time = time() reader = FlatFileParser() report = reader.parseGenericReport(input_file, keyTag='Row Names', header=None, unique=True) e_read_time = time() - s_read_time print "Reading time [%s]" %(e_read_time) new_report = Report() c_names = report.getColumnNames() r_names = report.getRowNames() s_reload_time = time() for r_name in r_names: print "reloading [%s]" % (r_name) for c_name in c_names: value = report.getElement(r_name, c_name) if value != None: new_report.addElement(r_name, c_name, value)