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)
