def test_get_chromosome_1_loop_through_size_20_lower_pval(self):
start = 0
size = 20
pval_interval = FloatInterval().set_tuple(0.00001, 0.00001)
looped_through = 1
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
datasets, index_marker = self.searcher.search_chromosome(
chromosome=1, start=start, size=size, pval_interval=pval_interval)
d = utils.extend_dsets_with_subset(d, datasets)
while len(datasets[REFERENCE_DSET]) > 0:
assert_studies_in_list(datasets, ['s1', 's3'])
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 20)
start = start + index_marker
datasets, index_marker = self.searcher.search_chromosome(
chromosome=1,
start=start,
size=size,
pval_interval=pval_interval)
d = utils.extend_dsets_with_subset(d, datasets)
looped_through += 1
assert looped_through == 5
# start changes on each loop!
assert index_marker == 0
# 80 unique variants
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET]) == 80
def test_loop_through_t2_size_42(self):
start = 0
size = 42
looped_through = 1
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
while True:
datasets, index_marker = self.searcher.search_trait(trait='t2',
start=start,
size=size)
d = utils.extend_dsets_with_subset(d, datasets)
if len(datasets[REFERENCE_DSET]) <= 0:
break
if looped_through <= 1:
assert_number_of_times_study_is_in_datasets(datasets, 's3', 42)
assert_studies_from_list(datasets, ['s3'])
elif looped_through == 2:
assert_number_of_times_study_is_in_datasets(datasets, 's3', 8)
assert_number_of_times_study_is_in_datasets(datasets, 's4', 34)
assert_studies_from_list(datasets, ['s3', 's4'])
else:
assert_number_of_times_study_is_in_datasets(datasets, 's4', 16)
assert_studies_from_list(datasets, ['s4'])
looped_through += 1
start = start + index_marker
assert looped_through == 4
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET])
def test_get_chromosome_1_loop_through_size_20_s3(self):
start = 0
size = 20
looped_through = 1
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
datasets, index_marker = self.searcher.search_chromosome(chromosome=1,
start=start,
size=size,
study='s3')
d = utils.extend_dsets_with_subset(d, datasets)
while len(datasets[REFERENCE_DSET]) > 0:
assert_studies_from_list(datasets, ['s3'])
if looped_through <= 2:
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 20)
else:
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 10)
start = start + index_marker
datasets, index_marker = self.searcher.search_chromosome(
chromosome=1, start=start, size=size, study='s3')
d = utils.extend_dsets_with_subset(d, datasets)
looped_through += 1
assert looped_through == 4
assert index_marker == 0
# 50 unique variants
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET]) == 50
def __init__(self,
snp,
start,
size,
config_properties=None,
chromosome=None):
self.snp = snp
self.chromosome = chromosome
self.start = start
self.size = size
self.properties = properties_handler.get_properties(config_properties)
self.search_path = properties_handler.get_search_path(self.properties)
self.chr_dir = self.properties.chr_dir
self.snp_dir = self.properties.snp_dir
self.bp_step = self.properties.bp_step
self.datasets = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
self.index_marker = 0
if chromosome is None:
self.service = self._calculate_snp_service()
else:
self.service = self._get_snp_service()
def test_loop_through_w_restrinction_and_always_get_size_20_results(self):
start = 0
size = 20
looped_through = 1
# s2 and s3 p-value limits
pval_interval = FloatInterval().set_tuple(0.0002, 0.06)
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
while True:
print("start", start)
datasets, next_index = self.searcher.search_all_assocs(
start=start, size=size, pval_interval=pval_interval)
print("next index", next_index)
print(datasets[STUDY_DSET])
d = utils.extend_dsets_with_subset(d, datasets)
if len(datasets[REFERENCE_DSET]) <= 0:
break
if looped_through <= 2:
assert_studies_from_list(datasets, ['s2'])
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 20)
elif looped_through == 3:
assert_studies_from_list(datasets, ['s2', 's3'])
assert_number_of_times_study_is_in_datasets(datasets, 's2', 10)
assert_number_of_times_study_is_in_datasets(datasets, 's3', 10)
else:
assert_studies_from_list(datasets, ['s3'])
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 20)
looped_through += 1
start = start + next_index
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET]) == 100
def test_loop_through_t2_size_5_w_restriction_to_s4(self):
start = 0
size = 5
looped_through = 1
pval_interval = FloatInterval().set_tuple(0.06, 0.3)
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
while True:
datasets, index_marker = self.searcher.search_trait(
trait='t2',
start=start,
size=size,
pval_interval=pval_interval)
d = utils.extend_dsets_with_subset(d, datasets)
if len(datasets[REFERENCE_DSET]) <= 0:
break
# already on the first loop I want to have reached s4
if looped_through == 1:
# all of s3 + the first 5 elements of s4
assert index_marker == 55
assert_number_of_times_study_is_in_datasets(datasets, 's4', 5)
assert_studies_from_list(datasets, ['s4'])
looped_through += 1
start = start + index_marker
assert looped_through == 11
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET])
def test_get_chr_1_second_range_loop_20_upper_pval(self):
start = 0
size = 20
# index 25-40 for first non-empty block: 48500000
# index 40-50 for second non-empty block: 49200000
bp_interval = IntInterval().set_string_tuple("1200001:49200000")
# index 20-35
pval_interval = FloatInterval().set_tuple(0.1, 0.1)
looped_through = 1
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
datasets, index_marker = self.searcher.search_chromosome(chromosome=1, start=start, size=size, bp_interval=bp_interval, pval_interval=pval_interval)
d = utils.extend_dsets_with_subset(d, datasets)
while len(datasets[REFERENCE_DSET]) > 0:
assert_studies_in_list(datasets, ['s1','s3'])
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 20)
start = start + index_marker
datasets, index_marker = self.searcher.search_chromosome(chromosome=1, start=start, size=size, bp_interval=bp_interval, pval_interval=pval_interval)
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 0)
d = utils.extend_dsets_with_subset(d, datasets)
looped_through += 1
assert looped_through == 2
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET]) == 20
def test_get_snp_loop_through_filter_lower_pval(self):
start = 0
size = 2
pval_interval = FloatInterval().set_tuple(0.01, 0.01)
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
datasets, index_marker = self.searcher.search_snp(
snp='rs138808727',
start=start,
size=size,
pval_interval=pval_interval)
d = utils.extend_dsets_with_subset(d, datasets)
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 2)
assert_studies_from_list(datasets, ['s1', 's3'])
assert index_marker == 6
start = start + index_marker
datasets, index_marker = self.searcher.search_snp(
snp='rs138808727',
start=start,
size=size,
pval_interval=pval_interval)
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 1)
assert_studies_from_list(datasets, ['s5'])
d = utils.extend_dsets_with_subset(d, datasets)
assert len(d[REFERENCE_DSET]) == 3
def test_create_dictionary_of_empty_dsets(self):
datasets = utils.create_dictionary_of_empty_dsets(['dset1', 'dset2'])
assert len(datasets) == 2
assert isinstance(datasets['dset1'], Dataset)
assert len(datasets['dset1']) == 0
assert isinstance(datasets['dset2'], Dataset)
assert len(datasets['dset2']) == 0
def __init__(self, start, size, config_properties=None):
self.starting_point = start
self.start = start
self.size = size
self.properties = properties_handler.get_properties(config_properties)
self.search_path = properties_handler.get_search_path(self.properties)
self.trait_dir = self.properties.trait_dir
self.datasets = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
# index marker will be returned along with the datasets
# it is the number that when added to the 'start' value that we started the query with
# will pinpoint where the next search needs to continue from
self.index_marker = self.search_traversed = 0
def test_get_all_loop_through_size_20(self):
start = 0
size = 20
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
datasets, index_marker = self.searcher.search_all_assocs(start=start, size=size)
d = utils.extend_dsets_with_subset(d, datasets)
while len(datasets[REFERENCE_DSET]) > 0:
if start + index_marker >= 240:
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 10)
else:
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 20)
start = start + index_marker
datasets, index_marker = self.searcher.search_all_assocs(start=start, size=size)
d = utils.extend_dsets_with_subset(d, datasets)
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET])
def __init__(self, chromosome, start, size, config_properties=None):
self.chromosome = chromosome
self.start = start
self.size = size
self.properties = properties_handler.get_properties(config_properties)
self.search_path = properties_handler.get_search_path(self.properties)
self.chr_dir = self.properties.chr_dir
self.datasets = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
self.index_marker = 0
self.h5file = fsutils.create_h5file_path(path=self.search_path, dir_name=self.chr_dir, file_name=chromosome)
if not os.path.isfile(self.h5file):
raise NotFoundError("Chromosome " + str(chromosome))
self.service = chromosome_service.ChromosomeService(self.h5file)
def test_get_snp_loop_through_size_1(self):
start = 0
size = 1
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
datasets, index_marker = self.searcher.search_snp(snp='rs138808727',
start=start,
size=size)
d = utils.extend_dsets_with_subset(d, datasets)
while len(datasets[REFERENCE_DSET]) > 0:
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 1)
start = start + index_marker
datasets, index_marker = self.searcher.search_snp(
snp='rs138808727', start=start, size=size)
d = utils.extend_dsets_with_subset(d, datasets)
assert len(d[REFERENCE_DSET]) == 5
def test_get_chr_1_second_range_loop_5(self):
start = 0
size = 5
bp_interval = IntInterval().set_string_tuple("1200001:49200000")
looped_through = 1
d = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
datasets, index_marker = self.searcher.search_chromosome(chromosome=1, start=start, size=size, bp_interval=bp_interval)
d = utils.extend_dsets_with_subset(d, datasets)
while len(datasets[REFERENCE_DSET]) > 0:
assert_studies_in_list(datasets, ['s1', 's3'])
assert_datasets_have_size(datasets, TO_QUERY_DSETS, 5)
start = start + index_marker
datasets, index_marker = self.searcher.search_chromosome(chromosome=1, start=start, size=size, bp_interval=bp_interval)
d = utils.extend_dsets_with_subset(d, datasets)
looped_through += 1
assert looped_through == 11
assert len(set(d[SNP_DSET])) == len(d[SNP_DSET])
def __init__(self, trait, start, size, config_properties=None):
self.trait = trait
self.start = start
self.size = size
self.properties = properties_handler.get_properties(config_properties)
self.search_path = properties_handler.get_search_path(self.properties)
self.trait_dir = self.properties.trait_dir
self.datasets = utils.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
# index marker will be returned along with the datasets
# it is the number that when added to the 'start' value that we started the query with
# will pinpoint where the next search needs to continue from
self.index_marker = 0
self.h5file = fsutils.create_h5file_path(self.search_path,
dir_name=self.trait_dir,
file_name=trait)
if not os.path.isfile(self.h5file):
raise NotFoundError("Trait " + trait)
self.service = study_service.StudyService(self.h5file)
def test_get_dsets_group(self):
chr_group_2 = gu.Group(self.f.get("/2"))
bp_interval = IntInterval().set_tuple(48500000, 48500000)
block = bk.Block(bp_interval)
block_groups = block.get_block_groups_from_parent(chr_group_2)
block_group = next(block_groups)
block_sub_groups = block_group.get_all_subgroups()
d = du.create_dictionary_of_empty_dsets(TO_QUERY_DSETS)
for block_sub_group in block_sub_groups:
datasets = query.get_dsets_from_group(block_sub_group, self.start,
self.size)
assert len(datasets) == len(TO_STORE_DSETS)
d = du.extend_dsets_with_subset(d, datasets)
for dset_name, dset in d.items():
if dset_name is STUDY_DSET:
assert len(set(dset)) == 3
else:
assert len(set(dset)) == 1
