def Run(self, args):
"""This is what gets called when the user runs this command.
Args:
args: an argparse namespace, All the arguments that were provided to this
command invocation.
Returns:
A list of reads that meet the search criteria.
"""
apitools_client = genomics_util.GetGenomicsClient()
messages = genomics_util.GetGenomicsMessages()
fields = genomics_util.GetQueryFields(self.GetReferencedKeyNames(args),
'alignments')
if fields:
global_params = messages.StandardQueryParameters(fields=fields)
else:
global_params = None
return list_pager.YieldFromList(
apitools_client.reads,
messages.SearchReadsRequest(
readGroupSetIds=[args.read_group_set_id],
referenceName=args.reference_name,
start=args.start,
end=args.end),
global_params=global_params,
limit=args.limit,
method='Search',
batch_size_attribute='pageSize',
batch_size=args.page_size,
field='alignments')
def Run(self, args):
"""This is what gets called when the user runs this command.
Args:
args: an argparse namespace, All the arguments that were provided to this
command invocation.
Returns:
A list of reads that meet the search criteria.
"""
genomics_util.ValidateLimitFlag(args.limit)
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
fields = genomics_util.GetQueryFields(self.GetReferencedKeyNames(args),
'alignments')
if fields:
global_params = messages.StandardQueryParameters(fields=fields)
else:
global_params = None
pager = list_pager.YieldFromList(
apitools_client.reads,
messages.SearchReadsRequest(
readGroupSetIds=[args.read_group_set_id],
referenceName=args.reference_name,
start=args.start,
end=args.end),
global_params=global_params,
limit=args.limit,
method='Search',
batch_size_attribute='pageSize',
batch_size=args.page_size,
field='alignments')
return genomics_util.ReraiseHttpExceptionPager(pager)
def Run(self, args):
"""This is what gets called when the user runs this command.
Args:
args: an argparse namespace, All the arguments that were provided to this
command invocation.
Yields:
A list of variants that meet the search criteria.
"""
apitools_client = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
fields = genomics_util.GetQueryFields(self.GetReferencedKeyNames(args),
'variants')
if fields:
global_params = genomics_messages.StandardQueryParameters(
fields=fields)
else:
global_params = None
variant_set_id = [args.variant_set_id] if args.variant_set_id else []
try:
for resource in list_pager.YieldFromList(
apitools_client.variants,
genomics_messages.SearchVariantsRequest(
variantSetIds=variant_set_id,
callSetIds=args.call_set_ids,
referenceName=args.reference_name,
start=args.start,
end=args.end,
maxCalls=args.limit_calls),
global_params=global_params,
limit=args.limit,
method='Search',
batch_size_attribute='pageSize',
batch_size=args.page_size,
field='variants'):
yield resource
except apitools_exceptions.HttpError as error:
msg = (
exceptions.HttpException(error).payload.status_message.replace(
'variantSetIds', '--variant-set-id').replace(
'callSetIds', '--call-set-ids').replace(
'referenceName', '--reference-name').replace(
'start', '--start').replace('end', '--end'))
raise exceptions.HttpException(msg)
def Run(self, args):
"""Run 'readgroupsets list'.
Args:
args: argparse.Namespace, The arguments that this command was invoked
with.
Returns:
The list of read group sets matching the given dataset ids.
Raises:
HttpException: An http error response was received while executing api
request.
"""
genomics_util.ValidateLimitFlag(args.limit)
apitools_client = self.context[lib.GENOMICS_APITOOLS_CLIENT_KEY]
req_class = (self.context[
lib.GENOMICS_MESSAGES_MODULE_KEY].SearchReadGroupSetsRequest)
messages = self.context[lib.GENOMICS_MESSAGES_MODULE_KEY]
fields = genomics_util.GetQueryFields(self.GetReferencedKeyNames(args),
'readGroupSets')
if fields:
global_params = messages.StandardQueryParameters(fields=fields)
else:
global_params = None
page_size = args.page_size
if args.limit and args.limit < page_size:
page_size = args.limit
pager = list_pager.YieldFromList(apitools_client.readgroupsets,
req_class(
name=args.name,
datasetIds=args.dataset_ids),
method='Search',
global_params=global_params,
limit=args.limit,
batch_size_attribute='pageSize',
batch_size=page_size,
field='readGroupSets')
return genomics_util.ReraiseHttpExceptionPager(pager)
def Run(self, args):
"""This is what gets called when the user runs this command.
Args:
args: an argparse namespace, All the arguments that were provided to this
command invocation.
Returns:
A list of variants that meet the search criteria.
"""
apitools_client = genomics_util.GetGenomicsClient()
genomics_messages = genomics_util.GetGenomicsMessages()
fields = genomics_util.GetQueryFields(self.GetReferencedKeyNames(args),
'variants')
if fields:
global_params = genomics_messages.StandardQueryParameters(
fields=fields)
else:
global_params = None
variant_set_id = [args.variant_set_id] if args.variant_set_id else []
pager = list_pager.YieldFromList(
apitools_client.variants,
genomics_messages.SearchVariantsRequest(
variantSetIds=variant_set_id,
callSetIds=args.call_set_ids,
referenceName=args.reference_name,
start=args.start,
end=args.end,
maxCalls=args.limit_calls),
global_params=global_params,
limit=args.limit,
method='Search',
batch_size_attribute='pageSize',
batch_size=args.page_size,
field='variants')
return genomics_util.ReraiseHttpExceptionPager(pager,
self.RewriteError)
def Run(self, args):
"""Run 'readgroupsets list'.
Args:
args: argparse.Namespace, The arguments that this command was invoked
with.
Returns:
The list of read group sets matching the given dataset ids.
Raises:
HttpException: An http error response was received while executing api
request.
"""
apitools_client = genomics_util.GetGenomicsClient()
messages = genomics_util.GetGenomicsMessages()
req_class = messages.SearchReadGroupSetsRequest
fields = genomics_util.GetQueryFields(
self.GetReferencedKeyNames(args), 'readGroupSets')
if fields:
global_params = messages.StandardQueryParameters(fields=fields)
else:
global_params = None
page_size = args.page_size
if args.limit and args.limit < page_size:
page_size = args.limit
return list_pager.YieldFromList(apitools_client.readgroupsets,
req_class(name=args.name,
datasetIds=args.dataset_ids),
method='Search',
global_params=global_params,
limit=args.limit,
batch_size_attribute='pageSize',
batch_size=page_size,
field='readGroupSets')