def test_translate_site_then_allele_marker(self):
result = list()
agg = PRGAggregator()
expected = [5, 6, 6]
for marker in expected:
result.append(agg.translate("ref", marker))
self.assertEqual(expected, result)
def test_translate_markers_across_multiple_references(self):
result = list()
agg = PRGAggregator()
for ref, markers in zip(["ref1", "ref2"], [[5, 6, 6]] * 2):
for marker in markers:
result.append(agg.translate(ref, marker))
expected = [5, 6, 6, 7, 8, 8]
self.assertEqual(expected, result)
def test_translate_site_marker_twice(self):
"""
Legacy format support: converts 5A6C5 to 5A6C6
"""
result = list()
agg = PRGAggregator()
result.append(agg.translate("ref", 5))
result.append(agg.translate("ref", 5))
expected = [5, 6]
self.assertEqual(expected, result)
def test_translate_site_marker_more_than_twice_fails(self):
# Single odd marker is used to encode a variant site
agg = PRGAggregator()
agg.translate("ref", 5)
agg.translate("ref", 5)
with self.assertRaises(PRGAggregationError):
agg.translate("ref", 5)
def test_first_allocated_marker_is_fixed(self):
# This should not happen in practice, first encountered
# marker should be 5, but is not this class's job to enforce
agg = PRGAggregator()
self.assertEqual(5, agg.translate("ref", 101))
def test_translate_allele_marker_without_site_marker_fails(self):
# Allele marker comes after site marker in encoding
agg = PRGAggregator()
with self.assertRaises(PRGAggregationError):
agg.translate("ref", 6)
def test_translate_non_variant_marker_fails(self):
# Variant markers are integers >=5
agg = PRGAggregator()
with self.assertRaises(PRGAggregationError):
agg.translate("ref", 4)
def setUp(self):
self.agg = PRGAggregator()