def setUp(self):
self.common_data = create_common_entities()
self.project = self.common_data['project']
self.pos_elem_tups = [
(968327, 'IS150'),
(1305482, 'IS150'),
(4517605, 'IS186')]
graph_test_dir = os.path.join(GF_TEST_DIR, 'graph_tests')
contig_alignment_bam = os.path.join(
graph_test_dir, 'contig_alignment.bam')
contig_alignment_to_me_bam = os.path.join(
graph_test_dir, 'contig_alignment_to_me.bam')
# Create graph
G = nx.DiGraph()
# Create sequence interval instances for reference and each contig
ref_intervals = SequenceIntervals(
'ref', 4622887, tag='ref')
G.ref_intervals = ref_intervals
add_alignment_to_graph(G, contig_alignment_bam)
add_me_alignment_to_graph(G, contig_alignment_to_me_bam)
self.me_iv_pairs = me_translocation_walk(G)
def setUp(self):
self.common_data = create_common_entities()
self.project = self.common_data['project']
self.pos_elem_tups = [(968327, 'IS150'), (1305482, 'IS150'),
(4517605, 'IS186')]
graph_test_dir = os.path.join(GF_TEST_DIR, 'graph_tests')
contig_alignment_bam = os.path.join(graph_test_dir,
'contig_alignment.bam')
contig_alignment_to_me_bam = os.path.join(
graph_test_dir, 'contig_alignment_to_me.bam')
# Create graph
G = nx.DiGraph()
# Create sequence interval instances for reference and each contig
ref_intervals = SequenceIntervals('ref', 4622887, tag='ref')
G.ref_intervals = ref_intervals
add_alignment_to_graph(G, contig_alignment_bam)
add_me_alignment_to_graph(G, contig_alignment_to_me_bam)
self.me_iv_pairs = me_translocation_walk(G)
def setUp(self):
common_entities = create_common_entities()
project = common_entities['project']
self.ref_genome_1 = common_entities['reference_genome']
self.chromosome = common_entities['chromosome']
self.sample_1 = ExperimentSample.objects.create(
project=project,
label=SAMPLE_1_LABEL)
# Create 100 variants with alts, positions 1 to 100.
# We add them to a fake VariantSet so that they show up in the
# materialized variant view table.
self.first_variant_position = 1
self.num_variants = 100
fake_variant_set = VariantSet.objects.create(
reference_genome=self.ref_genome_1,
label='fake')
alignment_group = AlignmentGroup.objects.create(
label='Alignment 1',
reference_genome=self.ref_genome_1,
aligner=AlignmentGroup.ALIGNER.BWA)
for position in xrange(self.first_variant_position,
self.first_variant_position + self.num_variants):
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=self.chromosome,
position=position,
ref_value='A')
variant.variantalternate_set.add(
VariantAlternate.objects.create(
variant=variant,
alt_value='G'))
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={})
VariantEvidence.objects.create(
experiment_sample=self.sample_1,
variant_caller_common_data=vccd,
data={})
VariantToVariantSet.objects.create(
variant=variant,
variant_set=fake_variant_set)
self.var_set1 = VariantSet.objects.create(
reference_genome=self.ref_genome_1,
label=VARIANTSET_1_LABEL)
self.var_set2 = VariantSet.objects.create(
reference_genome=self.ref_genome_1,
label=VARIANTSET_2_LABEL)
def setUp(self):
self.common_entities = create_common_entities()
self.ref_genome = import_reference_genome_from_local_file(
self.common_entities['project'], 'ref_genome', TEST_FASTA,
'fasta')
ref_genome_source = self.ref_genome.dataset_set.get(
type=Dataset.TYPE.REFERENCE_GENOME_FASTA)\
.get_absolute_location()
with open(ref_genome_source) as fh:
self.ref_genome_seq_record = SeqIO.read(fh, 'fasta')
def setUp(self):
common_entities = create_common_entities()
project = common_entities['project']
self.ref_genome_1 = common_entities['reference_genome']
self.chromosome = common_entities['chromosome']
self.sample_1 = ExperimentSample.objects.create(project=project,
label=SAMPLE_1_LABEL)
# Create 100 variants with alts, positions 1 to 100.
# We add them to a fake VariantSet so that they show up in the
# materialized variant view table.
self.first_variant_position = 1
self.num_variants = 100
fake_variant_set = VariantSet.objects.create(
reference_genome=self.ref_genome_1, label='fake')
alignment_group = AlignmentGroup.objects.create(
label='Alignment 1',
reference_genome=self.ref_genome_1,
aligner=AlignmentGroup.ALIGNER.BWA)
for position in xrange(self.first_variant_position,
self.first_variant_position +
self.num_variants):
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=self.chromosome,
position=position,
ref_value='A')
variant.variantalternate_set.add(
VariantAlternate.objects.create(variant=variant,
alt_value='G'))
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={})
VariantEvidence.objects.create(experiment_sample=self.sample_1,
variant_caller_common_data=vccd,
data={})
VariantToVariantSet.objects.create(variant=variant,
variant_set=fake_variant_set)
self.var_set1 = VariantSet.objects.create(
reference_genome=self.ref_genome_1, label=VARIANTSET_1_LABEL)
self.var_set2 = VariantSet.objects.create(
reference_genome=self.ref_genome_1, label=VARIANTSET_2_LABEL)
def setUp(self):
common_entities = create_common_entities()
self.project = common_entities['project']
self.reference_genome = import_reference_genome_from_local_file(
self.project, 'ref_genome', TEST_FASTA, 'fasta')
self.experiment_sample = ExperimentSample.objects.create(
project=self.project, label='sample1')
copy_and_add_dataset_source(self.experiment_sample,
Dataset.TYPE.FASTQ1, Dataset.TYPE.FASTQ1,
TEST_FASTQ1)
copy_and_add_dataset_source(self.experiment_sample,
Dataset.TYPE.FASTQ2, Dataset.TYPE.FASTQ2,
TEST_FASTQ2)
def setUp(self):
"""Override.
"""
self.common_entities = create_common_entities()
self.ref_genome = self.common_entities['reference_genome']
def setUp(self):
self.common_data = create_common_entities()
self.project = self.common_data['project']
def setUp(self):
self.common_entities = create_common_entities()
self.cursor = connection.cursor()
def setUp(self):
self.test_entities = create_common_entities()
self.reference_genome = self.test_entities['reference_genome']
def setUp(self):
self.common_data = create_common_entities()
self.project = self.common_data['project']
self.reference_genome = import_reference_genome_from_local_file(
self.project, 'ref_genome', TEST_FASTA, 'fasta')
def setUp(self):
"""Override.
"""
common_entities = create_common_entities()
self.user = common_entities['user']
def test_simple(self):
common_entities = create_common_entities()
project = common_entities['project']
self.ref_genome_1 = common_entities['reference_genome']
self.chromosome = common_entities['chromosome']
self.sample_1 = ExperimentSample.objects.create(
project=project,
label=SAMPLE_1_LABEL)
self.sample_2 = ExperimentSample.objects.create(
project=project,
label=SAMPLE_2_LABEL)
alignment_group = AlignmentGroup.objects.create(
label='Alignment 1',
reference_genome=self.ref_genome_1,
aligner=AlignmentGroup.ALIGNER.BWA)
var_set_1 = VariantSet.objects.create(
reference_genome=self.ref_genome_1,
label=VARIANTSET_1_LABEL)
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=self.chromosome,
position=100,
ref_value='A')
variant.variantalternate_set.add(
VariantAlternate.objects.create(
variant=variant,
alt_value='G'))
vtvs = VariantToVariantSet.objects.create(
variant=variant,
variant_set=var_set_1)
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={})
# Add a VariantEvidence with no GT_TYPE.
VariantEvidence.objects.create(
experiment_sample=self.sample_1,
variant_caller_common_data=vccd,
data={})
self.assertEqual(0, vtvs.sample_variant_set_association.count())
# Now add a VariantEvidence that has GT_TYPE=2 and run
# ensure_variant_set_consistency().
raw_sample_data_dict = {
'CALLED': True,
'GT_TYPE': 2,
'GT_BASES': 'G/G'
}
VariantEvidence.objects.create(
experiment_sample=self.sample_2,
variant_caller_common_data=vccd,
data=raw_sample_data_dict)
ensure_variant_set_consistency(var_set_1)
self.assertEqual(1, vtvs.sample_variant_set_association.count())
def setUp(self):
self.common_data = create_common_entities()
self.project = self.common_data['project']
def setUp(self):
self.common_entities = create_common_entities()
def test_add_variants_to_set_from_bed(self):
common_entities = create_common_entities()
project = common_entities['project']
self.ref_genome_1 = common_entities['reference_genome']
alignment_group = AlignmentGroup.objects.create(
label='Alignment 1',
reference_genome=self.ref_genome_1,
aligner=AlignmentGroup.ALIGNER.BWA)
(self.sample_1, created) = ExperimentSample.objects.get_or_create(
project=project,
label=SAMPLE_1_LABEL)
sample_alignment = ExperimentSampleToAlignment.objects.create(
alignment_group=alignment_group,
experiment_sample=self.sample_1)
# Create variants in the bed regions from best_test.bed
for var_poor_map in range(20):
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=Chromosome.objects.get(reference_genome=self.ref_genome_1),
position=random.randint(101,200),
ref_value='A')
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={}
)
for var_no_cov in range(20):
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=Chromosome.objects.get(reference_genome=self.ref_genome_1),
position=random.randint(301,400),
ref_value='A')
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={}
)
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=Chromosome.objects.get(reference_genome=self.ref_genome_1),
position=random.randint(501,600),
ref_value='A')
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={}
)
new_bed_path = copy_dataset_to_entity_data_dir(
entity= sample_alignment,
original_source_location= TEST_BED)
bed_dataset = add_dataset_to_entity(sample_alignment,
dataset_label= Dataset.TYPE.BED_CALLABLE_LOCI,
dataset_type= Dataset.TYPE.BED_CALLABLE_LOCI,
filesystem_location= new_bed_path)
vs_to_v_map = add_variants_to_set_from_bed(
sample_alignment, bed_dataset)
variant_set_labels = set([vs.label for vs in vs_to_v_map.keys()])
self.assertEqual(set(['POOR_MAPPING_QUALITY', 'NO_COVERAGE']),
variant_set_labels)
for variant_set, variants in vs_to_v_map.items():
for v in variants:
# POOR MAPPING QUAL should be from 101 to 200
if variant_set.label == 'POOR_MAPPING_QUALITY':
self.assertTrue(v.position in pyinter.closedopen(
101, 200))
# NO COVERAGE should be from 301 to 400, 501 to 600
elif variant_set.label == 'NO_COVERAGE':
self.assertTrue(v.position in pyinter.IntervalSet([
pyinter.closedopen(301,400),
pyinter.closedopen(501,600)]))
else:
raise AssertionError(
'bad variant set %s made.' % variant_set.label)
def setUp(self):
"""Override.
"""
self.common_entities = create_common_entities()
def setUp(self):
"""Override.
"""
common_entities = create_common_entities()
self.user = common_entities['user']
def setUp(self):
self.common_entities = create_common_entities()
def setUp(self):
"""Override.
"""
self.common_entities = create_common_entities()
self.project = self.common_entities['project']
def test_add_variants_to_set_from_bed(self):
common_entities = create_common_entities()
project = common_entities['project']
self.ref_genome_1 = common_entities['reference_genome']
alignment_group = AlignmentGroup.objects.create(
label='Alignment 1',
reference_genome=self.ref_genome_1,
aligner=AlignmentGroup.ALIGNER.BWA)
(self.sample_1, created) = ExperimentSample.objects.get_or_create(
project=project, label=SAMPLE_1_LABEL)
sample_alignment = ExperimentSampleToAlignment.objects.create(
alignment_group=alignment_group, experiment_sample=self.sample_1)
# Create variants in the bed regions from best_test.bed
for var_poor_map in range(20):
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=Chromosome.objects.get(
reference_genome=self.ref_genome_1),
position=random.randint(101, 200),
ref_value='A')
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={})
for var_no_cov in range(20):
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=Chromosome.objects.get(
reference_genome=self.ref_genome_1),
position=random.randint(301, 400),
ref_value='A')
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={})
variant = Variant.objects.create(
type=Variant.TYPE.TRANSITION,
reference_genome=self.ref_genome_1,
chromosome=Chromosome.objects.get(
reference_genome=self.ref_genome_1),
position=random.randint(501, 600),
ref_value='A')
vccd = VariantCallerCommonData.objects.create(
variant=variant,
source_dataset_id=1,
alignment_group=alignment_group,
data={})
new_bed_path = copy_dataset_to_entity_data_dir(
entity=sample_alignment, original_source_location=TEST_BED)
bed_dataset = add_dataset_to_entity(
sample_alignment,
dataset_label=Dataset.TYPE.BED_CALLABLE_LOCI,
dataset_type=Dataset.TYPE.BED_CALLABLE_LOCI,
filesystem_location=new_bed_path)
vs_to_v_map = add_variants_to_set_from_bed(sample_alignment,
bed_dataset)
variant_set_labels = set([vs.label for vs in vs_to_v_map.keys()])
self.assertEqual(set(['POOR_MAPPING_QUALITY', 'NO_COVERAGE']),
variant_set_labels)
for variant_set, variants in vs_to_v_map.items():
for v in variants:
# POOR MAPPING QUAL should be from 101 to 200
if variant_set.label == 'POOR_MAPPING_QUALITY':
self.assertTrue(v.position in pyinter.closedopen(101, 200))
# NO COVERAGE should be from 301 to 400, 501 to 600
elif variant_set.label == 'NO_COVERAGE':
self.assertTrue(v.position in pyinter.IntervalSet([
pyinter.closedopen(301, 400),
pyinter.closedopen(501, 600)
]))
else:
raise AssertionError('bad variant set %s made.' %
variant_set.label)
def setUp(self):
self.test_entities = create_common_entities()
self.reference_genome = self.test_entities['reference_genome']
def setUp(self):
"""Override.
"""
self.common_entities = create_common_entities()
self.ref_genome = self.common_entities['reference_genome']
def setUp(self):
"""Override.
"""
self.common_entities = create_common_entities()
self.project = self.common_entities['project']
def setUp(self):
"""Override.
"""
self.common_entities = create_common_entities()