def test_cuffnorm(self):
collection = self.res.collection.create(name='Test collection')
# pylint: disable=unbalanced-tuple-unpacking
cuffquant_1, cuffquant_2, cuffquant_3, cuffquant_4 = self.get_cuffquants(4, collection)
# pylint: enable=unbalanced-tuple-unpacking
gff = self.get_gtf(1)
group = collection.create_group_relation(
samples=[cuffquant_1.sample, cuffquant_2.sample],
label='replicates'
)
group1 = collection.create_group_relation(
samples=[cuffquant_3.sample, cuffquant_4.sample],
label='replicates'
)
# Run cuffnorm on a collection
cuffnorm = collection.run_cuffnorm(annotation=gff)
self.assertEqual(
cuffnorm.input['cuffquant'],
[cuffquant_1.id, cuffquant_2.id, cuffquant_3.id, cuffquant_4.id]
)
self.assertEqual(cuffnorm.input['annotation'], gff.id)
self.assertEqual(cuffnorm.input['replicates'], ['0', '0', '1', '1'])
# Run cuffnorm on a two groups of replicates in collection
cuffnorm = expressions.cuffnorm([group1, group], annotation=gff)
self.assertEqual(
cuffnorm.input['cuffquant'],
[cuffquant_3.id, cuffquant_4.id, cuffquant_1.id, cuffquant_2.id]
)
self.assertEqual(cuffnorm.input['annotation'], gff.id)
self.assertEqual(cuffnorm.input['replicates'], ['0', '0', '1', '1'])
def test_cuffnorm(self):
collection = self.res.collection.create(name='Test collection')
# pylint: disable=unbalanced-tuple-unpacking
cuffquant_1, cuffquant_2, cuffquant_3, cuffquant_4 = self.get_cuffquants(4, collection)
# pylint: enable=unbalanced-tuple-unpacking
annotation = self.get_gtf()
group = collection.create_group_relation(
samples=[cuffquant_1.sample, cuffquant_2.sample],
category='replicates'
)
group1 = collection.create_group_relation(
samples=[cuffquant_3.sample, cuffquant_4.sample],
category='clones'
)
# Run cuffnorm on a collection
cuffnorm = collection.run_cuffnorm(annotation=annotation)
self.assertEqual(
cuffnorm.input['cuffquant'],
[cuffquant_1.id, cuffquant_2.id, cuffquant_3.id, cuffquant_4.id]
)
self.assertEqual(cuffnorm.input['annotation'], annotation.id)
self.assertEqual(cuffnorm.input['replicates'], ['0', '0', '1', '1'])
# Run cuffnorm on two groups of replicates in collection
cuffnorm = expressions.cuffnorm([group1, group], annotation=annotation)
self.assertEqual(
cuffnorm.input['cuffquant'],
[cuffquant_3.id, cuffquant_4.id, cuffquant_1.id, cuffquant_2.id]
)
self.assertEqual(cuffnorm.input['annotation'], annotation.id)
self.assertEqual(cuffnorm.input['replicates'], ['0', '0', '1', '1'])
def test_cuffnorm(self):
collection = self.res.collection.create(name='Test collection')
# pylint: disable=unbalanced-tuple-unpacking
cuffquant_1, cuffquant_2, cuffquant_3, cuffquant_4 = self.get_cuffquants(
4, collection)
# pylint: enable=unbalanced-tuple-unpacking
annotation = self.get_gtf()
group = collection.create_group_relation(
samples=[
cuffquant_1.sample,
cuffquant_2.sample,
cuffquant_3.sample,
cuffquant_4.sample,
],
labels=['1', '1', '2', '2'],
category='replicates',
)
# Run cuffnorm on a collection
cuffnorm = collection.run_cuffnorm(annotation=annotation)
self.assertEqual(
cuffnorm.input['cuffquant'],
[cuffquant_1.id, cuffquant_2.id, cuffquant_3.id, cuffquant_4.id])
self.assertEqual(cuffnorm.input['annotation'], annotation.id)
# Run cuffnorm on two groups of replicates in collection
cuffnorm = expressions.cuffnorm(group, annotation=annotation)
self.assertEqual(
cuffnorm.input['cuffquant'],
[cuffquant_1.id, cuffquant_2.id, cuffquant_3.id, cuffquant_4.id])
self.assertEqual(cuffnorm.input['annotation'], annotation.id)