本文整理汇总了Python中xbrowse.Variant类的典型用法代码示例。如果您正苦于以下问题:Python Variant类的具体用法?Python Variant怎么用?Python Variant使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Variant类的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: get_variants_from_note_tuples
def get_variants_from_note_tuples(project, note_tuples):
variants = []
for note_t in note_tuples:
variant = get_datastore(project.project_id).get_single_variant(
project.project_id, note_t[3], note_t[0], note_t[1], note_t[2]
)
if not variant:
variant = Variant(note_t[0], note_t[1], note_t[2])
get_annotator().annotate_variant(variant, project.get_reference_population_slugs())
# variant.annotation = get_annotator().get_variant(note_t[0], note_t[1], note_t[2])
variant.set_extra("family_id", note_t[3])
variant.set_extra("project_id", project.project_id)
variants.append(variant)
return variants
开发者ID:batsal,项目名称:xbrowse,代码行数:14,代码来源:lookups.py
示例2: mendelian_variant_search_spec
def mendelian_variant_search_spec(request):
project, family = get_project_and_family_for_user(request.user, request.GET)
# TODO: use form
search_hash = request.GET.get('search_hash')
search_spec_dict, variants = cache_utils.get_cached_results(project.project_id, search_hash)
search_spec = MendelianVariantSearchSpec.fromJSON(search_spec_dict)
if variants is None:
variants = api_utils.calculate_mendelian_variant_search(search_spec, family.xfamily())
else:
variants = [Variant.fromJSON(v) for v in variants]
add_extra_info_to_variants_family(get_reference(), family, variants)
return_type = request.GET.get('return_type')
if return_type == 'json' or not return_type:
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_spec': search_spec_dict,
})
elif request.GET.get('return_type') == 'csv':
response = HttpResponse(content_type='text/csv')
response['Content-Disposition'] = 'attachment; filename="results_{}.csv"'.format(search_hash)
writer = csv.writer(response)
indiv_ids = family.indiv_ids_with_variant_data()
headers = xbrowse_displays.get_variant_display_headers(get_mall(project.project_id), project, indiv_ids)
writer.writerow(headers)
for variant in variants:
fields = xbrowse_displays.get_display_fields_for_variant(get_mall(project.project_id), project, variant, indiv_ids)
writer.writerow(fields)
return response
开发者ID:frichter,项目名称:seqr,代码行数:32,代码来源:views.py
示例3: get_single_variant
def get_single_variant(self, project_id, family_id, xpos, ref, alt):
collection = self._get_family_collection(project_id, family_id)
variant = collection.find_one({'xpos': xpos, 'ref': ref, 'alt': alt})
if variant:
return Variant.fromJSON(variant)
else:
return None
开发者ID:statcgx,项目名称:xbrowse,代码行数:8,代码来源:mongo_datastore.py
示例4: get_variants
def get_variants(self, project_id, family_id, genotype_filter=None, variant_filter=None):
db_query = _make_db_query(genotype_filter, variant_filter)
collection = self._get_family_collection(project_id, family_id)
for variant_dict in collection.find(db_query).sort('xpos'):
variant = Variant.fromJSON(variant_dict)
if passes_variant_filter(variant, variant_filter)[0]:
yield variant
开发者ID:statcgx,项目名称:xbrowse,代码行数:8,代码来源:mongo_datastore.py
示例5: get_variants_in_range
def get_variants_in_range(self, project_id, family_id, xpos_start, xpos_end):
collection = self._get_family_collection(project_id, family_id)
if not collection:
raise ValueError("Family not found: " + str(family_id))
for variant_dict in collection.find({'$and': [{'xpos': {'$gte': xpos_start}}, {'xpos': {'$lte': xpos_end}}]}):
variant = Variant.fromJSON(variant_dict)
self.add_annotations_to_variant(variant, project_id)
yield variant
开发者ID:burkesquires,项目名称:xbrowse,代码行数:8,代码来源:mongo_datastore.py
示例6: get_variants_from_variant_tuples
def get_variants_from_variant_tuples(project, variant_tuples, user=None):
datastore = get_datastore(project)
population_slugs = project.get_reference_population_slugs()
variant_tuples_by_family_id = {}
for xpos, ref, alt, family_id in variant_tuples:
if family_id not in variant_tuples_by_family_id:
variant_tuples_by_family_id[family_id] = []
variant_tuples_by_family_id[family_id].append((xpos, ref, alt))
variants = []
for family_id, variant_tuples in variant_tuples_by_family_id.items():
variants_for_family = datastore.get_multiple_variants(
project.project_id,
family_id,
variant_tuples,
user=user
)
for (xpos, ref, alt), variant in zip(variant_tuples, variants_for_family):
if not variant:
variant = Variant(xpos, ref, alt)
get_annotator().annotate_variant(variant, population_slugs)
variant.set_extra('created_variant', True)
variant.set_extra('family_id', family_id)
variant.set_extra('project_id', project.project_id)
variants.append(variant)
return variants
开发者ID:macarthur-lab,项目名称:seqr,代码行数:29,代码来源:lookups.py
示例7: get_variants_cohort
def get_variants_cohort(self, project_id, cohort_id, variant_filter=None):
db_query = self._make_db_query(None, variant_filter)
collection = self._get_family_collection(project_id, cohort_id)
for i, variant in enumerate(collection.find(db_query).sort('xpos').limit(settings.VARIANT_QUERY_RESULTS_LIMIT+5)):
if i > settings.VARIANT_QUERY_RESULTS_LIMIT:
raise Exception("ERROR: this search exceeded the %s variant result size limit. Please set additional filters and try again." % settings.VARIANT_QUERY_RESULTS_LIMIT)
yield Variant.fromJSON(variant)
开发者ID:macarthur-lab,项目名称:seqr,代码行数:9,代码来源:mongo_datastore.py
示例8: get_variants_from_variant_tuples
def get_variants_from_variant_tuples(project, variant_tuples):
variants = []
for t in variant_tuples:
variant = get_datastore(project.project_id).get_single_variant(
project.project_id,
t[3],
t[0],
t[1],
t[2]
)
if not variant:
variant = Variant(t[0], t[1], t[2])
get_annotator().annotate_variant(variant, project.get_reference_population_slugs())
variant.set_extra('family_id', t[3])
variant.set_extra('project_id', project.project_id)
variants.append(variant)
return variants
开发者ID:burkesquires,项目名称:xbrowse,代码行数:18,代码来源:lookups.py
示例9: get_single_variant
def get_single_variant(self, project_id, family_id, xpos, ref, alt, user=None):
collection = self._get_family_collection(project_id, family_id)
if not collection:
return None
variant_dict = collection.find_one({'xpos': xpos, 'ref': ref, 'alt': alt})
if variant_dict:
variant = Variant.fromJSON(variant_dict)
self.add_annotations_to_variants([variant], project_id, family_id=family_id)
return variant
else:
return None
开发者ID:macarthur-lab,项目名称:seqr,代码行数:11,代码来源:mongo_datastore.py
示例10: get_variants_in_range
def get_variants_in_range(self, project_id, family_id, xpos_start, xpos_end):
collection = self._get_family_collection(project_id, family_id)
if not collection:
raise ValueError("Family not found: " + str(family_id))
for i, variant_dict in enumerate(collection.find({'$and': [{'xpos': {'$gte': xpos_start}}, {'xpos': {'$lte': xpos_end}}]}).limit(MONGO_QUERY_RESULTS_LIMIT+5)):
if i > MONGO_QUERY_RESULTS_LIMIT:
raise Exception("ERROR: this search exceeded the %s variant result size limit. Please set additional filters and try again." % MONGO_QUERY_RESULTS_LIMIT)
variant = Variant.fromJSON(variant_dict)
self.add_annotations_to_variant(variant, project_id)
yield variant
开发者ID:mattsolo1,项目名称:seqr,代码行数:11,代码来源:mongo_datastore.py
示例11: get_variants
def get_variants(self, project_id, family_id, genotype_filter=None, variant_filter=None):
db_query = self._make_db_query(genotype_filter, variant_filter)
collection = self._get_family_collection(project_id, family_id)
if not collection:
print("Error: mongodb collection not found for project %s family %s " % (project_id, family_id))
return
for variant_dict in collection.find(db_query).sort('xpos'):
variant = Variant.fromJSON(variant_dict)
self.add_annotations_to_variant(variant, project_id)
if passes_variant_filter(variant, variant_filter)[0]:
yield variant
开发者ID:burkesquires,项目名称:xbrowse,代码行数:12,代码来源:mongo_datastore.py
示例12: get_variants
def get_variants(self, project_id, variant_filter=None):
variant_filter_t = VariantFilter(**(variant_filter if variant_filter else {}))
db_query = self._make_db_query(None, variant_filter)
collection = self._get_project_collection(project_id)
for variant_dict in collection.find(db_query).sort('xpos'):
variant = Variant.fromJSON(variant_dict)
if variant_filter is None:
yield variant
if passes_variant_filter(variant, variant_filter_t)[0]:
yield variant
开发者ID:ericminikel,项目名称:xbrowse,代码行数:12,代码来源:project_datastore.py
示例13: get_variants
def get_variants(self, project_id, family_id, genotype_filter=None, variant_filter=None):
db_query = self._make_db_query(genotype_filter, variant_filter)
collection = self._get_family_collection(project_id, family_id)
if not collection:
print("Error: mongodb collection not found for project %s family %s " % (project_id, family_id))
return
for i, variant_dict in enumerate(collection.find(db_query).sort('xpos').limit(MONGO_QUERY_RESULTS_LIMIT+5)):
if i >= MONGO_QUERY_RESULTS_LIMIT:
raise Exception("ERROR: this search exceeded the %s variant result size limit. Please set additional filters and try again." % MONGO_QUERY_RESULTS_LIMIT)
variant = Variant.fromJSON(variant_dict)
self.add_annotations_to_variant(variant, project_id)
if passes_variant_filter(variant, variant_filter)[0]:
yield variant
开发者ID:mattsolo1,项目名称:seqr,代码行数:15,代码来源:mongo_datastore.py
示例14: get_variants
def get_variants(self, project_id, family_id, genotype_filter=None, variant_filter=None, quality_filter=None, indivs_to_consider=None, user=None):
db_query = self._make_db_query(genotype_filter, variant_filter)
collection = self._get_family_collection(project_id, family_id)
if not collection:
logger.error("Error: mongodb collection not found for project %s family %s " % (project_id, family_id))
return
for i, variant_dict in enumerate(collection.find({'$and' : [{k: v} for k, v in db_query.items()]}).sort('xpos').limit(settings.VARIANT_QUERY_RESULTS_LIMIT+5)):
if i >= settings.VARIANT_QUERY_RESULTS_LIMIT:
raise Exception("ERROR: this search exceeded the %s variant result size limit. Please set additional filters and try again." % settings.VARIANT_QUERY_RESULTS_LIMIT)
variant = Variant.fromJSON(variant_dict)
variant.set_extra('project_id', project_id)
variant.set_extra('family_id', family_id)
self.add_annotations_to_variants([variant], project_id)
if passes_variant_filter(variant, variant_filter)[0]:
yield variant
开发者ID:macarthur-lab,项目名称:seqr,代码行数:17,代码来源:mongo_datastore.py
示例15: get_variants_in_gene
def get_variants_in_gene(self, project_id, gene_id, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = self._make_db_query(None, modified_variant_filter)
collection = self._get_project_collection(project_id)
variants = []
for variant_dict in collection.find(db_query).hint([('gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)]):
variant = Variant.fromJSON(variant_dict)
if passes_variant_filter(variant, modified_variant_filter):
variants.append(variant)
variants = sorted(variants, key=lambda v: v.unique_tuple())
return variants
开发者ID:ericminikel,项目名称:xbrowse,代码行数:18,代码来源:project_datastore.py
示例16: cohort_variant_search_spec
def cohort_variant_search_spec(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
# TODO: use form
search_spec_dict, variants = cache_utils.get_cached_results(project.project_id, request.GET.get('search_hash'))
search_spec = MendelianVariantSearchSpec.fromJSON(search_spec_dict)
if variants is None:
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
else:
variants = [Variant.fromJSON(v) for v in variants]
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_spec': search_spec.toJSON(),
})
开发者ID:frichter,项目名称:seqr,代码行数:19,代码来源:views.py
示例17: get_project_variants_in_gene
def get_project_variants_in_gene(self, project_id, gene_id, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = self._make_db_query(None, modified_variant_filter)
logger.info("Project Gene Search: " + str(project_id) + " all variants query: " + str(db_query))
collection = self._get_project_collection(project_id)
# we have to collect list in memory here because mongo can't sort on xpos,
# as result size can get too big.
# need to find a better way to do this.
variants = [Variant.fromJSON(variant_dict) for variant_dict in collection.find(db_query).hint([('db_gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)])]
self.add_annotations_to_variants(variants, project_id)
variants = filter(lambda variant: passes_variant_filter(variant, modified_variant_filter), variants)
variants = sorted(variants, key=lambda v: v.unique_tuple())
return variants
开发者ID:macarthur-lab,项目名称:seqr,代码行数:19,代码来源:mongo_datastore.py
示例18: get_variants_in_gene
def get_variants_in_gene(self, project_id, family_id, gene_id, genotype_filter=None, variant_filter=None):
if variant_filter is None:
modified_variant_filter = VariantFilter()
else:
modified_variant_filter = copy.deepcopy(variant_filter)
modified_variant_filter.add_gene(gene_id)
db_query = _make_db_query(genotype_filter, modified_variant_filter)
collection = self._get_family_collection(project_id, family_id)
# we have to collect list in memory here because mongo can't sort on xpos,
# as result size can get too big.
# need to find a better way to do this.
variants = []
for variant_dict in collection.find(db_query).hint([('gene_ids', pymongo.ASCENDING), ('xpos', pymongo.ASCENDING)]):
variant = Variant.fromJSON(variant_dict)
if passes_variant_filter(variant, modified_variant_filter):
variants.append(variant)
variants = sorted(variants, key=lambda v: v.unique_tuple())
for v in variants:
yield v
开发者ID:statcgx,项目名称:xbrowse,代码行数:22,代码来源:mongo_datastore.py
示例19: get_elasticsearch_variants
def get_elasticsearch_variants(
self,
project_id,
family_id=None,
variant_filter=None,
genotype_filter=None,
variant_id_filter=None,
quality_filter=None,
indivs_to_consider=None,
include_all_consequences=False,
user=None,
max_results_limit=settings.VARIANT_QUERY_RESULTS_LIMIT,
):
from xbrowse_server.base.models import Project, Family, Individual
from seqr.models import Sample
from seqr.utils.es_utils import _liftover_grch38_to_grch37
from xbrowse_server.mall import get_reference
redis_client = None
if settings.REDIS_SERVICE_HOSTNAME:
try:
redis_client = redis.StrictRedis(host=settings.REDIS_SERVICE_HOSTNAME, socket_connect_timeout=3)
redis_client.ping()
except redis.exceptions.TimeoutError as e:
logger.warn("Unable to connect to redis host: {}".format(settings.REDIS_SERVICE_HOSTNAME) + str(e))
redis_client = None
cache_key = "Variants___%s___%s___%s" % (
project_id,
family_id,
json.dumps([
variant_filter.toJSON() if variant_filter else None,
genotype_filter,
quality_filter,
variant_id_filter,
indivs_to_consider,
include_all_consequences,
])
)
cached_results = redis_client and redis_client.get(cache_key)
if cached_results is not None:
variant_results = json.loads(cached_results)
return [Variant.fromJSON(variant_json) for variant_json in variant_results]
if family_id is None:
project = Project.objects.get(project_id=project_id)
elasticsearch_index = project.get_elasticsearch_index()
logger.info("Searching in project elasticsearch index: " + str(elasticsearch_index))
else:
family = Family.objects.get(project__project_id=project_id, family_id=family_id)
elasticsearch_index = family.get_elasticsearch_index()
project = family.project
logger.info("Searching in family elasticsearch index: " + str(elasticsearch_index))
if indivs_to_consider is None and genotype_filter and not family_id:
indivs_to_consider = genotype_filter.keys()
individuals = Individual.objects.filter(family__project__project_id=project_id).only("indiv_id", "seqr_individual")
if indivs_to_consider:
individuals = individuals.filter(indiv_id__in=indivs_to_consider)
if family_id is not None:
individuals = individuals.filter(family__family_id=family_id)
if not indivs_to_consider:
indivs_to_consider = [i.indiv_id for i in individuals]
prefetch_related_objects(individuals, "seqr_individual")
es_indices = [index.rstrip('*') for index in elasticsearch_index.split(',')]
samples = Sample.objects.filter(
individual__in=[i.seqr_individual for i in individuals if i.seqr_individual],
dataset_type=Sample.DATASET_TYPE_VARIANT_CALLS,
sample_status=Sample.SAMPLE_STATUS_LOADED,
elasticsearch_index__startswith=es_indices[0],
loaded_date__isnull=False,
).order_by('-loaded_date')
prefetch_related_objects(samples, "individual")
family_individual_ids_to_sample_ids = {}
for i in individuals:
indiv_id = i.indiv_id
sample_id = None
if i.seqr_individual:
sample_id = next((
sample.sample_id for sample in samples
if sample.individual == i.seqr_individual and sample.elasticsearch_index.startswith(tuple(es_indices))
), None)
family_individual_ids_to_sample_ids[indiv_id] = sample_id or indiv_id
query_json = self._make_db_query(genotype_filter, variant_filter)
es_client = elasticsearch.Elasticsearch(host=settings.ELASTICSEARCH_SERVICE_HOSTNAME, timeout=30)
mapping = es_client.indices.get_mapping(str(elasticsearch_index) + "*")
index_fields = {}
is_parent_child = False
is_nested = False
if elasticsearch_index in mapping and 'join_field' in mapping[elasticsearch_index]["mappings"]["variant"]["properties"]:
# Nested indices are not sharded so all samples are in the single index
logger.info("matching indices: " + str(elasticsearch_index))
is_parent_child = True
#.........这里部分代码省略.........
开发者ID:macarthur-lab,项目名称:seqr,代码行数:101,代码来源:elasticsearch_datastore.py
示例20: add_or_edit_variant_note
def add_or_edit_variant_note(request):
"""Add a variant note"""
family = None
if 'family_id' in request.GET:
project, family = get_project_and_family_for_user(request.user, request.GET)
else:
project = utils.get_project_for_user(request.user, request.GET)
form = api_forms.VariantNoteForm(project, request.GET)
if not form.is_valid():
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
variant = get_datastore(project.project_id).get_single_variant(
project.project_id,
family.family_id,
form.cleaned_data['xpos'],
form.cleaned_data['ref'],
form.cleaned_data['alt'],
)
if not variant:
variant = Variant.fromJSON({
'xpos' : form.cleaned_data['xpos'], 'ref': form.cleaned_data['ref'], 'alt': form.cleaned_data['alt'],
'genotypes': {}, 'extras': {},
})
if 'note_id' in form.cleaned_data and form.cleaned_data['note_id']:
event_type = "edit_variant_note"
notes = VariantNote.objects.filter(
id=form.cleaned_data['note_id'],
project=project,
xpos=form.cleaned_data['xpos'],
ref=form.cleaned_data['ref'],
alt=form.cleaned_data['alt'],
)
if not notes:
return JSONResponse({
'is_error': True,
'error': 'note id %s not found' % form.cleaned_data['note_id']
})
note = notes[0]
note.user = request.user
note.note = form.cleaned_data['note_text']
note.date_saved = timezone.now()
if family:
note.family = family
note.save()
else:
event_type = "add_variant_note"
VariantNote.objects.create(
user=request.user,
project=project,
xpos=form.cleaned_data['xpos'],
ref=form.cleaned_data['ref'],
alt=form.cleaned_data['alt'],
note=form.cleaned_data['note_text'],
date_saved=timezone.now(),
family=family,
)
add_extra_info_to_variants_family(get_reference(), family, [variant,])
try:
settings.EVENTS_COLLECTION.insert({
'event_type': event_type,
'date': timezone.now(),
'project_id': ''.join(project.project_id),
'family_id': family.family_id,
'note': form.cleaned_data['note_text'],
'xpos':form.cleaned_data['xpos'],
'pos':variant.pos,
'chrom': variant.chr,
'ref':form.cleaned_data['ref'],
'alt':form.cleaned_data['alt'],
'gene_names': ", ".join(variant.extras['gene_names'].values()),
'username': request.user.username,
'email': request.user.email,
})
except Exception as e:
logging.error("Error while logging %s event: %s" % (event_type, e))
return JSONResponse({
'is_error': False,
'variant': variant.toJSON(),
})
开发者ID:mattsolo1,项目名称:seqr,代码行数:93,代码来源:views.py
注:本文中的xbrowse.Variant类示例由纯净天空整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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