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')