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 _test_variant_count_report(self, group):
'''Test variant summary counts queries, grouped by region.'''
report = self.variant_dao.variant_count_report(group)
output = StringIO.StringIO()
report.save(output)
str1 = output.getvalue()
output.close()
output = StringIO.StringIO()
report.save(output)
report2 = VariantSummaryReport.load(iter(output.getvalue().split('\n')[:-1]))
output.close()
output = StringIO.StringIO()
report2.save(output)
str2 = output.getvalue()
assert_equal(str1, str2, 'Saving-loading-saving doesn\'t give the same serialization as saving')
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 _test_variant_count_report(self, group):
'''Test variant summary counts queries, grouped by region.'''
report = self.variant_dao.variant_count_report(group)
output = StringIO.StringIO()
report.save(output)
str1 = output.getvalue()
output.close()
output = StringIO.StringIO()
report.save(output)
report2 = VariantSummaryReport.load(
iter(output.getvalue().split('\n')[:-1]))
output.close()
output = StringIO.StringIO()
report2.save(output)
str2 = output.getvalue()
assert_equal(
str1, str2,
'Saving-loading-saving doesn\'t give the same serialization as saving'
)
