def test_compound_non_commutative(self):
"""The goal is to test the non-cummutativity of applying compound het then some other filter,
or the contrary.
Not certain about the final number, but at least it should go without an error."""
variants = variants_collection_factory(db='test')
ss = samples_selection_factory(db='test',
groups={
'affected': ['09818', '09819'],
'not_affected': ['09960', '09961']
})
filter_coll = variant_filters_collection_factory([
('filter', '=', 'PASS'),
('aaf_1kg_all', '<=', '0.01'),
('genotype', '=', 'compound_het'),
], ss)
var = filter_coll.apply(variants).variants
self.assertEqual(len(var), 13)
filter_coll = variant_filters_collection_factory([
('genotype', '=', 'compound_het'),
('filter', '=', 'PASS'),
('aaf_1kg_all', '<=', '0.01'),
], ss)
var = filter_coll.apply(variants).variants
self.assertEqual(len(var), 0)
def setUp(self):
self.varCol = variants_collection_factory('test')
self.simpleVariants = VariantsCollection([
Variant(ref=x[0], quality=x[1], chrom=x[2], start=x[3])
for x in ([
('A', 100.3, 'chr1', 100), ('B', 10.4, 'chr1', 99), ('C', 9.2, 'chr2', 20),
('D', 200, 'chr12', 1000), ('E', 1, 'chr1', 2000),
])
])
def setUp(self):
self.varCol = variants_collection_factory('test')
self.simpleVariants = VariantsCollection([
Variant(ref=x[0], quality=x[1], chrom=x[2], start=x[3]) for x in ([
('A', 100.3, 'chr1', 100),
('B', 10.4, 'chr1', 99),
('C', 9.2, 'chr2', 20),
('D', 200, 'chr12', 1000),
('E', 1, 'chr1', 2000),
])
])
def test_compound_Lucie_FNDC1(self):
"""These 2(3) variants are annotated on different transcripts of the same gene,
and because of the group_by(transcript_id), the compound was not found.
Check here that it is fixed.
"""
ss = samples_selection_factory(db='test',
groups = {'affected': ['101563','101591'], 'not_affected':['101564','101565']})
variants = variants_collection_factory(db='test',
qs=Variant.objects.using('test').filter(gene_symbol='FNDC1'))
## To select them directly:
#variants = variants_collection_factory(
# Variants.objects.using('test').filter(start__in=['159653504','159653634']), db='test')
var = GenotypesFilterCompoundHeterozygous(ss).apply(variants).variants
self.assertEqual(len(var), 3)
def test_Xlinked_Norine_BMX(self):
"""This gene has no X-linked variant"""
db = 'lgueneau'
ss = samples_selection_factory(db=db,
groups = {'affected': ['09818','09819'], 'not_affected':['09960','09961']})
qs = Variant.objects.using(db).filter(gene_symbol__in=['BMX'], chrom='chrX')
# Using GenotypesFilterXLinked.apply()
variants = variants_collection_factory(db=db, qs=qs)
var = GenotypesFilterXLinked(ss).apply(variants).variants
self.assertEqual(len(var), 0)
# Using FilterCollection.apply()
fc = FiltersCollection([GenotypesFilterXLinked(ss)])
var = fc.apply(initqs=qs, db=db).variants
self.assertEqual(len(var), 0)
def test_Xlinked_Lucie_ASMTL(self):
"""This gene has 2 X-linked variants"""
db = 'lgueneau'
ss = samples_selection_factory(db=db,
groups = {'affected': ['09818','09819'], 'not_affected':['09960','09961']})
qs = Variant.objects.using(db).filter(gene_symbol__in=['ASMTL','CSF2RA','PPP2R3B','TM4SF2'], chrom='chrX')
# Using GenotypesFilterXLinked.apply()
variants = variants_collection_factory(db=db, qs=qs)
print(GenotypesFilterXLinked(ss).conditions_vector)
var = GenotypesFilterXLinked(ss).apply(variants).variants
self.assertEqual(len(var), 5)
# Using FilterCollection.apply()
fc = FiltersCollection([GenotypesFilterXLinked(ss)])
var = fc.apply(initqs=qs, db=db).variants
self.assertEqual(len(var), 5)
def test_Xlinked_Norine_BMX(self):
"""This gene has no X-linked variant"""
db = 'lgueneau'
ss = samples_selection_factory(db=db,
groups={
'affected': ['09818', '09819'],
'not_affected': ['09960', '09961']
})
qs = Variant.objects.using(db).filter(gene_symbol__in=['BMX'],
chrom='chrX')
# Using GenotypesFilterXLinked.apply()
variants = variants_collection_factory(db=db, qs=qs)
var = GenotypesFilterXLinked(ss).apply(variants).variants
self.assertEqual(len(var), 0)
# Using FilterCollection.apply()
fc = FiltersCollection([GenotypesFilterXLinked(ss)])
var = fc.apply(initqs=qs, db=db).variants
self.assertEqual(len(var), 0)
def test_compound_Lucie_FNDC1(self):
"""These 2(3) variants are annotated on different transcripts of the same gene,
and because of the group_by(transcript_id), the compound was not found.
Check here that it is fixed.
"""
ss = samples_selection_factory(db='test',
groups={
'affected': ['101563', '101591'],
'not_affected':
['101564', '101565']
})
variants = variants_collection_factory(
db='test',
qs=Variant.objects.using('test').filter(gene_symbol='FNDC1'))
## To select them directly:
#variants = variants_collection_factory(
# Variants.objects.using('test').filter(start__in=['159653504','159653634']), db='test')
var = GenotypesFilterCompoundHeterozygous(ss).apply(variants).variants
self.assertEqual(len(var), 3)
def test_Xlinked_Lucie_ASMTL(self):
"""This gene has 2 X-linked variants"""
db = 'lgueneau'
ss = samples_selection_factory(db=db,
groups={
'affected': ['09818', '09819'],
'not_affected': ['09960', '09961']
})
qs = Variant.objects.using(db).filter(
gene_symbol__in=['ASMTL', 'CSF2RA', 'PPP2R3B', 'TM4SF2'],
chrom='chrX')
# Using GenotypesFilterXLinked.apply()
variants = variants_collection_factory(db=db, qs=qs)
print(GenotypesFilterXLinked(ss).conditions_vector)
var = GenotypesFilterXLinked(ss).apply(variants).variants
self.assertEqual(len(var), 5)
# Using FilterCollection.apply()
fc = FiltersCollection([GenotypesFilterXLinked(ss)])
var = fc.apply(initqs=qs, db=db).variants
self.assertEqual(len(var), 5)
def test_compound_non_commutative(self):
"""The goal is to test the non-cummutativity of applying compound het then some other filter,
or the contrary.
Not certain about the final number, but at least it should go without an error."""
variants = variants_collection_factory(db='test')
ss = samples_selection_factory(db='test',
groups = {'affected': ['09818','09819'], 'not_affected':['09960','09961']})
filter_coll = variant_filters_collection_factory([
('filter', '=', 'PASS'),
('aaf_1kg_all', '<=', '0.01'),
('genotype', '=', 'compound_het'),
], ss)
var = filter_coll.apply(variants).variants
self.assertEqual(len(var), 13)
filter_coll = variant_filters_collection_factory([
('genotype', '=', 'compound_het'),
('filter', '=', 'PASS'),
('aaf_1kg_all', '<=', '0.01'),
], ss)
var = filter_coll.apply(variants).variants
self.assertEqual(len(var), 0)
def setUp(self):
self.ss = samples_selection_factory(TESTDB, groups='ped')
self.variants = variants_collection_factory(TESTDB)
self.N = len(self.variants)
def setUp(self):
self.variants = variants_collection_factory(db='test')
self.genotypes = genotypes_service(db='test').genotypes
def setUp(self):
self.variants = variants_collection_factory(db='test')
def test_sort_all(self):
"""Just check that it does not raise an error."""
var = variants_collection_factory(db='test')
for field in VARIANT_FIELDS:
Sort(field, False).sort(var)
def setUp(self):
self.rf = RequestFactory()
self.variants_django = Variants.objects.using('test').all()
self.variants = variants_collection_factory(db='test')
def setUp(self):
self.testdb = 'test'
self.variants = variants_collection_factory(self.testdb)
self.N = len(self.variants)
def test_sort_all(self):
"""Just check that it does not raise an error."""
var = variants_collection_factory(db='test')
for field in VARIANT_FIELDS:
Sort(field, False).sort(var)
def setUp(self):
self.variants = variants_collection_factory('test')
self.v1 = self.variants[0]
self.v8 = self.variants[8]
def setUp(self):
self.qs = Variant.objects.using('test')
self.variants = variants_collection_factory(db='test')
self.N = len(self.variants)
def setUp(self):
self.qs = Variant.objects.using('test')
self.variants = variants_collection_factory(db='test')
self.N = len(self.variants)
def setUp(self):
self.variants = variants_collection_factory('test')
self.N = len(self.variants)
def setUp(self):
self.testdb = 'test'
self.variants = variants_collection_factory(self.testdb)
self.N = len(self.variants)
def setUp(self):
self.rf = RequestFactory()
self.variants_django = Variants.objects.using('test').all()
self.variants = variants_collection_factory(db='test')
def setUp(self):
self.variants = variants_collection_factory('test')
self.N = len(self.variants)
def setUp(self):
self.ss = samples_selection_factory(TESTDB, groups='ped')
self.variants = variants_collection_factory(TESTDB)
self.N = len(self.variants)
def setUp(self):
self.variants = variants_collection_factory(db='test')
self.genotypes = genotypes_service(db='test').genotypes
def setUp(self):
self.var = variants_collection_factory(db='test')
self.ss = samples_selection_factory(db='test')
def setUp(self):
self.variants = variants_collection_factory(db='test')
def setUp(self):
self.variants = variants_collection_factory('test')
self.v1 = self.variants[0]
self.v8 = self.variants[8]
