def test_nonVariantSites_singleAllelePerBlock(self):
prg_seq = 'ACTGT5A6T6A5CC7CA8T7CC'
regions = prg.parse(prg_seq)
for region in regions:
if not region.is_variant_site:
self.assertEqual(len(region.alleles), 1)
def test_noVariantSites_oneAlleleBlock(self):
prg_seq = 'ACTGTCCTC'
regions = prg.parse(prg_seq)
region = [region for region in regions][0]
result = [''.join(x) for x in region.alleles]
expected = ['ACTGTCCTC']
self.assertEqual(result, expected)
def test_threeVariantAlleles_orderedInAlleleAttr(self):
prg_seq = 'TT5A6T6AA5CC'
regions = prg.parse(prg_seq)
variant_site_block = [
region for region in regions if region.is_variant_site
][0]
expected = ['A', 'T', 'AA']
result = [''.join(x) for x in variant_site_block.alleles]
self.assertEqual(result, expected)
def test_twoVariantSites_correctVariantMarkers(self):
prg_seq = 'ACTGT5A6T6A5CC7CA8T7CC'
regions = prg.parse(prg_seq)
variant_markers = []
for region in regions:
if region.is_variant_site:
variant_markers.append(region.variant_site_marker)
expected = ['5', '7']
self.assertEqual(variant_markers, expected)
def test_bothEdgesMultiCharVarSiteMarker_correctBlocks(self):
prg_seq = '97AC98GT97'
regions = prg.parse(prg_seq)
expected = [
['AC', 'GT'],
]
for region, expected in zip(regions, expected):
result = [''.join(x) for x in region.alleles]
self.assertEqual(result, expected)
def test_singleVariantSite_singleVariantBlock(self):
prg_seq = '5A6T5'
regions = prg.parse(prg_seq)
expected = [
['A', 'T'],
]
for region, expected in zip(regions, expected):
result = [''.join(x) for x in region.alleles]
self.assertEqual(result, expected)
def test_bothEdgesVariantSite_correctBlocks(self):
prg_seq = '5A6T5AA7C8A7'
regions = prg.parse(prg_seq)
expected = [
['A', 'T'], # first variant site
['AA'],
['C', 'A'], # second variant site
]
for region, expected in zip(regions, expected):
result = [''.join(x) for x in region.alleles]
self.assertEqual(result, expected)
def test_noVariantSites_oneBlock(self):
prg_seq = 'ACTGTCCTC'
regions = prg.parse(prg_seq)
regions = [region for region in regions]
self.assertEqual(len(regions), 1)
def test_twoVariantSites_correctNumVariantSites(self):
prg_seq = 'AC5A6T6A5CC7CA8T7CC'
regions = prg.parse(prg_seq)
num_variant_sites = sum(region.is_variant_site for region in regions)
self.assertEqual(num_variant_sites, 2)
