def main(parser):
wwarnCalcDict = {}
config = ConfigParser.RawConfigParser()
config.read(parser.config_file)
ageGroups = parseAgeGroups(config.get('GENERAL', 'age_groups'))
copyNumberGroups = parseCopyNumberGroups(config.get('GENERAL', 'copy_number_groups'))
(markerGroups, markerCombos) = parseMarkerList(parser.marker_list)
dataIter = createMysqlIterator(config, parser.study_ids, parser.sites, copyNumberGroups, markerCombos, parser.year_step)
calculateWWARNStatistics(wwarnCalcDict, dataIter, ageGroups)
# Before we can print our output we need to group all our statistics together under the
# categories and labels found in our marker map
ageLabels = [t[2] for t in ageGroups]
groupedStats = generateGroupedStatistics(wwarnCalcDict, markerGroups, ageLabels)
# Our statistics need to be written to two files:
# 1.) Statistics not grouped by age
# 2.) Statistics grouped by age
allFile = join(parser.output_directory, parser.output_prefix + '.all.calcs')
ageFile = join(parser.output_directory, parser.output_prefix + '.age.calcs')
write_statistics_to_file(groupedStats, allFile, ['All'], parser.year_step, parser.debug)
write_statistics_to_file(groupedStats, ageFile, ageLabels, parser.year_step, parser.debug)
