class TestHuttDao(unittest.TestCase):
#---------------------------------------------
# Constants
#---------------------------------------------
TEST_URL = 'mysql://*****:*****@127.0.0.1/hutt' # Should be built from $OBER/testdata/annotate/data.mysql.qc.10000 using the create-annotation-db script
#---------------------------------------------
# Setup Methods
#---------------------------------------------
def setUp(self):
'''Use a localhost UCSC copy.'''
self.variant_dao = VariantDao(TestHuttDao.TEST_URL)
def tearDown(self):
'''Drop the database.'''
pass
#---------------------------------------------
# Test Methods
#---------------------------------------------
def test_num_records(self):
'''Test getting the total # of SNP records.'''
assert_equal(self.variant_dao.num_records(), 10000, 'Wrong row count from SNP table')
def test_variant_count(self):
'''Test variant summary counts queries.'''
maf = np.concatenate((np.arange(0, 0.11, 0.01), [0.5]))
for i in xrange(len(maf) - 1):
result = Counter(dict((REGION_CATEGORY_OF[k], v) for k, v in self.variant_dao.variant_count_report_maf_bin('region', maf[i], maf[i + 1])))
self.assertTrue(max(result.itervalues()) > 0, 'No non-trivial variant category count found in result dictionary')
def test_variant_count_report_region(self):
'''Test variant summary counts queries, grouped by region.'''
self._test_variant_count_report('region')
def test_variant_count_report_coding(self):
'''Test variant summary counts queries, grouped by coding.'''
self._test_variant_count_report('coding')
#---------------------------------------------
# Private Methods
#---------------------------------------------
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 setUp(self):
'''Use a localhost UCSC copy.'''
self.variant_dao = VariantDao(TestHuttDao.TEST_URL)
def setUp(self):
'''Use a localhost UCSC copy.'''
self.variant_dao = VariantDao(TestHuttDao.TEST_URL)
class TestHuttDao(unittest.TestCase):
#---------------------------------------------
# Constants
#---------------------------------------------
TEST_URL = 'mysql://*****:*****@127.0.0.1/hutt' # Should be built from $OBER/testdata/annotate/data.mysql.qc.10000 using the create-annotation-db script
#---------------------------------------------
# Setup Methods
#---------------------------------------------
def setUp(self):
'''Use a localhost UCSC copy.'''
self.variant_dao = VariantDao(TestHuttDao.TEST_URL)
def tearDown(self):
'''Drop the database.'''
pass
#---------------------------------------------
# Test Methods
#---------------------------------------------
def test_num_records(self):
'''Test getting the total # of SNP records.'''
assert_equal(self.variant_dao.num_records(), 10000,
'Wrong row count from SNP table')
def test_variant_count(self):
'''Test variant summary counts queries.'''
maf = np.concatenate((np.arange(0, 0.11, 0.01), [0.5]))
for i in xrange(len(maf) - 1):
result = Counter(
dict((REGION_CATEGORY_OF[k], v)
for k, v in self.variant_dao.variant_count_report_maf_bin(
'region', maf[i], maf[i + 1])))
self.assertTrue(
max(result.itervalues()) > 0,
'No non-trivial variant category count found in result dictionary'
)
def test_variant_count_report_region(self):
'''Test variant summary counts queries, grouped by region.'''
self._test_variant_count_report('region')
def test_variant_count_report_coding(self):
'''Test variant summary counts queries, grouped by coding.'''
self._test_variant_count_report('coding')
#---------------------------------------------
# Private Methods
#---------------------------------------------
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'
)
