def generate_reports_for_paper(db_url='mysql://*****:*****@127.0.0.1/hutt', save_dir=os.environ['OBER'] + '/doc/paper_impute/supplementary'): '''Generate all variant reports (data file + bar charts) for imputation paper using the database whose connection is specified by the URL ''db_url''.''' # Load data from file for group in ('region', 'coding'): variant_dao = VariantDao(db_url) # report = variant_dao.variant_count_report(group) # report.save(open('%s/variant-count-%s.dat' % (save_dir, group), 'wb')) report = VariantSummaryReport.load( open('%s/variant-count-%s.dat' % (save_dir, group), 'rb')) # Generate figure variant_summary_bar_chart(report) # Save figure to file for extension in ('png', 'eps'): plt.savefig('%s/variant-count-%s.%s' % (save_dir, group, extension))
def setUp(self): '''Use a localhost UCSC copy.''' self.variant_dao = VariantDao(TestHuttDao.TEST_URL)