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
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)
