""" NCBI Datasets API ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 1 API is considred stable and will not be subject to breaking changes. However, certain endpoints will be [deprecated](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/reference-docs/rest-api/deprecated_apis/), and then sunset as newer versions are published. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/how-tos/genomes/large-download/), and retrieve the individual data files at a later time. # noqa: E501 The version of the OpenAPI document: v1 Generated by: https://openapi-generator.tech """ import re # noqa: F401 import sys # noqa: F401 from ncbi.datasets.openapi.api_client import ApiClient, Endpoint as _Endpoint from ncbi.datasets.openapi.model_utils import ( # noqa: F401 check_allowed_values, check_validations, date, datetime, file_type, none_type, validate_and_convert_types ) from ncbi.datasets.openapi.model.rpc_status import RpcStatus from ncbi.datasets.openapi.model.v1_download_summary import V1DownloadSummary from ncbi.datasets.openapi.model.v1_fasta import V1Fasta from ncbi.datasets.openapi.model.v1_gene_dataset_request import V1GeneDatasetRequest from ncbi.datasets.openapi.model.v1_gene_dataset_request_content_type import V1GeneDatasetRequestContentType from ncbi.datasets.openapi.model.v1_gene_dataset_request_sort_field import V1GeneDatasetRequestSortField from ncbi.datasets.openapi.model.v1_gene_match import V1GeneMatch from ncbi.datasets.openapi.model.v1_gene_metadata import V1GeneMetadata from ncbi.datasets.openapi.model.v1_organism import V1Organism from ncbi.datasets.openapi.model.v1_organism_query_request_tax_rank_filter import V1OrganismQueryRequestTaxRankFilter from ncbi.datasets.openapi.model.v1_organism_query_request_taxon_resource_filter import V1OrganismQueryRequestTaxonResourceFilter from ncbi.datasets.openapi.model.v1_ortholog_request_content_type import V1OrthologRequestContentType from ncbi.datasets.openapi.model.v1_ortholog_set import V1OrthologSet from ncbi.datasets.openapi.model.v1_sci_name_and_ids import V1SciNameAndIds from ncbi.datasets.openapi.model.v1_sort_direction import V1SortDirection class GeneApi(object): """NOTE: This class is auto generated by OpenAPI Generator Ref: https://openapi-generator.tech Do not edit the class manually. """ def __init__(self, api_client=None): if api_client is None: api_client = ApiClient() self.api_client = api_client self.download_gene_package_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/id/{gene_ids}/download', 'operation_id': 'download_gene_package', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'gene_ids', 'include_annotation_type', 'fasta_filter', 'filename', ], 'required': [ 'gene_ids', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'gene_ids': ([int],), 'include_annotation_type': ([V1Fasta],), 'fasta_filter': ([str],), 'filename': (str,), }, 'attribute_map': { 'gene_ids': 'gene_ids', 'include_annotation_type': 'include_annotation_type', 'fasta_filter': 'fasta_filter', 'filename': 'filename', }, 'location_map': { 'gene_ids': 'path', 'include_annotation_type': 'query', 'fasta_filter': 'query', 'filename': 'query', }, 'collection_format_map': { 'gene_ids': 'csv', 'include_annotation_type': 'multi', 'fasta_filter': 'multi', } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [], }, api_client=api_client ) self.download_gene_package_post_endpoint = _Endpoint( settings={ 'response_type': (file_type,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/download', 'operation_id': 'download_gene_package_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_gene_dataset_request', 'filename', ], 'required': [ 'v1_gene_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_gene_dataset_request': (V1GeneDatasetRequest,), 'filename': (str,), }, 'attribute_map': { 'filename': 'filename', }, 'location_map': { 'v1_gene_dataset_request': 'body', 'filename': 'query', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/zip', 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.gene_download_summary_by_accession_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/accession/{accessions}/download_summary', 'operation_id': 'gene_download_summary_by_accession', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'fasta_filter', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'fasta_filter': ([str],), }, 'attribute_map': { 'accessions': 'accessions', 'fasta_filter': 'fasta_filter', }, 'location_map': { 'accessions': 'path', 'fasta_filter': 'query', }, 'collection_format_map': { 'accessions': 'csv', 'fasta_filter': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_download_summary_by_id_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/id/{gene_ids}/download_summary', 'operation_id': 'gene_download_summary_by_id', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'gene_ids', 'fasta_filter', ], 'required': [ 'gene_ids', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'gene_ids': ([int],), 'fasta_filter': ([str],), }, 'attribute_map': { 'gene_ids': 'gene_ids', 'fasta_filter': 'fasta_filter', }, 'location_map': { 'gene_ids': 'path', 'fasta_filter': 'query', }, 'collection_format_map': { 'gene_ids': 'csv', 'fasta_filter': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_download_summary_by_post_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/download_summary', 'operation_id': 'gene_download_summary_by_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_gene_dataset_request', ], 'required': [ 'v1_gene_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_gene_dataset_request': (V1GeneDatasetRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_gene_dataset_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.gene_download_summary_by_tax_and_symbol_endpoint = _Endpoint( settings={ 'response_type': (V1DownloadSummary,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/symbol/{symbols}/taxon/{taxon}/download_summary', 'operation_id': 'gene_download_summary_by_tax_and_symbol', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'symbols', 'taxon', 'fasta_filter', ], 'required': [ 'symbols', 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'symbols': ([str],), 'taxon': (str,), 'fasta_filter': ([str],), }, 'attribute_map': { 'symbols': 'symbols', 'taxon': 'taxon', 'fasta_filter': 'fasta_filter', }, 'location_map': { 'symbols': 'path', 'taxon': 'path', 'fasta_filter': 'query', }, 'collection_format_map': { 'symbols': 'csv', 'fasta_filter': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_metadata_by_accession_endpoint = _Endpoint( settings={ 'response_type': (V1GeneMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/accession/{accessions}', 'operation_id': 'gene_metadata_by_accession', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'accessions', 'returned_content', 'sort_schema_field', 'sort_schema_direction', 'limit', ], 'required': [ 'accessions', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'accessions': ([str],), 'returned_content': (V1GeneDatasetRequestContentType,), 'sort_schema_field': (V1GeneDatasetRequestSortField,), 'sort_schema_direction': (V1SortDirection,), 'limit': (str,), }, 'attribute_map': { 'accessions': 'accessions', 'returned_content': 'returned_content', 'sort_schema_field': 'sort_schema.field', 'sort_schema_direction': 'sort_schema.direction', 'limit': 'limit', }, 'location_map': { 'accessions': 'path', 'returned_content': 'query', 'sort_schema_field': 'query', 'sort_schema_direction': 'query', 'limit': 'query', }, 'collection_format_map': { 'accessions': 'csv', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_metadata_by_id_endpoint = _Endpoint( settings={ 'response_type': (V1GeneMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/id/{gene_ids}', 'operation_id': 'gene_metadata_by_id', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'gene_ids', 'returned_content', 'sort_schema_field', 'sort_schema_direction', 'limit', ], 'required': [ 'gene_ids', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'gene_ids': ([int],), 'returned_content': (V1GeneDatasetRequestContentType,), 'sort_schema_field': (V1GeneDatasetRequestSortField,), 'sort_schema_direction': (V1SortDirection,), 'limit': (str,), }, 'attribute_map': { 'gene_ids': 'gene_ids', 'returned_content': 'returned_content', 'sort_schema_field': 'sort_schema.field', 'sort_schema_direction': 'sort_schema.direction', 'limit': 'limit', }, 'location_map': { 'gene_ids': 'path', 'returned_content': 'query', 'sort_schema_field': 'query', 'sort_schema_direction': 'query', 'limit': 'query', }, 'collection_format_map': { 'gene_ids': 'csv', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_metadata_by_post_endpoint = _Endpoint( settings={ 'response_type': (V1GeneMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene', 'operation_id': 'gene_metadata_by_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_gene_dataset_request', ], 'required': [ 'v1_gene_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_gene_dataset_request': (V1GeneDatasetRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_gene_dataset_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.gene_metadata_by_tax_and_symbol_endpoint = _Endpoint( settings={ 'response_type': (V1GeneMetadata,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/symbol/{symbols}/taxon/{taxon}', 'operation_id': 'gene_metadata_by_tax_and_symbol', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'symbols', 'taxon', 'accessions', 'returned_content', 'sort_schema_field', 'sort_schema_direction', 'limit', ], 'required': [ 'symbols', 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'symbols': ([str],), 'taxon': (str,), 'accessions': ([str],), 'returned_content': (V1GeneDatasetRequestContentType,), 'sort_schema_field': (V1GeneDatasetRequestSortField,), 'sort_schema_direction': (V1SortDirection,), 'limit': (str,), }, 'attribute_map': { 'symbols': 'symbols', 'taxon': 'taxon', 'accessions': 'accessions', 'returned_content': 'returned_content', 'sort_schema_field': 'sort_schema.field', 'sort_schema_direction': 'sort_schema.direction', 'limit': 'limit', }, 'location_map': { 'symbols': 'path', 'taxon': 'path', 'accessions': 'query', 'returned_content': 'query', 'sort_schema_field': 'query', 'sort_schema_direction': 'query', 'limit': 'query', }, 'collection_format_map': { 'symbols': 'csv', 'accessions': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_metadata_stream_by_post_endpoint = _Endpoint( settings={ 'response_type': (V1GeneMatch,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/stream', 'operation_id': 'gene_metadata_stream_by_post', 'http_method': 'POST', 'servers': None, }, params_map={ 'all': [ 'v1_gene_dataset_request', ], 'required': [ 'v1_gene_dataset_request', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'v1_gene_dataset_request': (V1GeneDatasetRequest,), }, 'attribute_map': { }, 'location_map': { 'v1_gene_dataset_request': 'body', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/x-ndjson', 'application/json' ], 'content_type': [ 'application/json' ] }, api_client=api_client ) self.gene_orthologs_by_id_endpoint = _Endpoint( settings={ 'response_type': (V1OrthologSet,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/id/{gene_id}/orthologs', 'operation_id': 'gene_orthologs_by_id', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'gene_id', 'returned_content', 'taxon_filter', ], 'required': [ 'gene_id', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'gene_id': (int,), 'returned_content': (V1OrthologRequestContentType,), 'taxon_filter': ([str],), }, 'attribute_map': { 'gene_id': 'gene_id', 'returned_content': 'returned_content', 'taxon_filter': 'taxon_filter', }, 'location_map': { 'gene_id': 'path', 'returned_content': 'query', 'taxon_filter': 'query', }, 'collection_format_map': { 'taxon_filter': 'multi', } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_tax_name_query_endpoint = _Endpoint( settings={ 'response_type': (V1SciNameAndIds,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/taxon_suggest/{taxon_query}', 'operation_id': 'gene_tax_name_query', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'taxon_query', 'tax_rank_filter', 'tax_resource_filter', ], 'required': [ 'taxon_query', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'taxon_query': (str,), 'tax_rank_filter': (V1OrganismQueryRequestTaxRankFilter,), 'tax_resource_filter': (V1OrganismQueryRequestTaxonResourceFilter,), }, 'attribute_map': { 'taxon_query': 'taxon_query', 'tax_rank_filter': 'tax_rank_filter', 'tax_resource_filter': 'tax_resource_filter', }, 'location_map': { 'taxon_query': 'path', 'tax_rank_filter': 'query', 'tax_resource_filter': 'query', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) self.gene_tax_tree_endpoint = _Endpoint( settings={ 'response_type': (V1Organism,), 'auth': [ 'ApiKeyAuthHeader' ], 'endpoint_path': '/gene/taxon/{taxon}/tree', 'operation_id': 'gene_tax_tree', 'http_method': 'GET', 'servers': None, }, params_map={ 'all': [ 'taxon', 'children_only', ], 'required': [ 'taxon', ], 'nullable': [ ], 'enum': [ ], 'validation': [ ] }, root_map={ 'validations': { }, 'allowed_values': { }, 'openapi_types': { 'taxon': (str,), 'children_only': (bool,), }, 'attribute_map': { 'taxon': 'taxon', 'children_only': 'children_only', }, 'location_map': { 'taxon': 'path', 'children_only': 'query', }, 'collection_format_map': { } }, headers_map={ 'accept': [ 'application/json' ], 'content_type': [], }, api_client=api_client ) def download_gene_package( self, gene_ids, **kwargs ): """Get a gene dataset by gene ID # noqa: E501 Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata by gene ID. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.download_gene_package(gene_ids, async_req=True) >>> result = thread.get() Args: gene_ids ([int]): NCBI gene ids Keyword Args: include_annotation_type ([V1Fasta]): Select additional types of annotation to include in the data package. If unset, no annotation is provided.. [optional] fasta_filter ([str]): Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [optional] filename (str): Output file name.. [optional] if omitted the server will use the default value of "ncbi_dataset.zip" _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: file_type If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['gene_ids'] = \ gene_ids headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.download_gene_package_endpoint.call_with_http_info(**kwargs) def download_gene_package_post( self, v1_gene_dataset_request, **kwargs ): """Get a gene dataset by POST # noqa: E501 Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata by POST. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.download_gene_package_post(v1_gene_dataset_request, async_req=True) >>> result = thread.get() Args: v1_gene_dataset_request (V1GeneDatasetRequest): Keyword Args: filename (str): Output file name.. [optional] if omitted the server will use the default value of "ncbi_dataset.zip" _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: file_type If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_gene_dataset_request'] = \ v1_gene_dataset_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.download_gene_package_post_endpoint.call_with_http_info(**kwargs) def gene_download_summary_by_accession( self, accessions, **kwargs ): """Get gene download summary by RefSeq Accession # noqa: E501 Get gene download summary by RefSeq Accession in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_download_summary_by_accession(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): RNA or Protein accessions. Keyword Args: fasta_filter ([str]): Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1DownloadSummary If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['accessions'] = \ accessions headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_download_summary_by_accession_endpoint.call_with_http_info(**kwargs) def gene_download_summary_by_id( self, gene_ids, **kwargs ): """Get gene download summary by GeneID # noqa: E501 Get a download summary by GeneID in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_download_summary_by_id(gene_ids, async_req=True) >>> result = thread.get() Args: gene_ids ([int]): NCBI gene ids Keyword Args: fasta_filter ([str]): Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1DownloadSummary If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['gene_ids'] = \ gene_ids headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_download_summary_by_id_endpoint.call_with_http_info(**kwargs) def gene_download_summary_by_post( self, v1_gene_dataset_request, **kwargs ): """Get gene download summary # noqa: E501 Get gene download summary in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_download_summary_by_post(v1_gene_dataset_request, async_req=True) >>> result = thread.get() Args: v1_gene_dataset_request (V1GeneDatasetRequest): Keyword Args: _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1DownloadSummary If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_gene_dataset_request'] = \ v1_gene_dataset_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_download_summary_by_post_endpoint.call_with_http_info(**kwargs) def gene_download_summary_by_tax_and_symbol( self, symbols, taxon, **kwargs ): """Get gene download summary by gene symbol # noqa: E501 Get gene download summary by gene symbol in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_download_summary_by_tax_and_symbol(symbols, taxon, async_req=True) >>> result = thread.get() Args: symbols ([str]): Gene symbol taxon (str): Taxon for provided gene symbol Keyword Args: fasta_filter ([str]): Limit the FASTA sequences in the datasets package to these transcript and protein accessions. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1DownloadSummary If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['symbols'] = \ symbols kwargs['taxon'] = \ taxon headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_download_summary_by_tax_and_symbol_endpoint.call_with_http_info(**kwargs) def gene_metadata_by_accession( self, accessions, **kwargs ): """Get gene metadata by RefSeq Accession # noqa: E501 Get detailed gene metadata by RefSeq Accession in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_metadata_by_accession(accessions, async_req=True) >>> result = thread.get() Args: accessions ([str]): RNA or Protein accessions. Keyword Args: returned_content (V1GeneDatasetRequestContentType): Return either gene-ids, or entire gene metadata. [optional] sort_schema_field (V1GeneDatasetRequestSortField): Select a field to sort on.. [optional] sort_schema_direction (V1SortDirection): Select a direction for the sort.. [optional] limit (str): Limit the number of returned results (\"all\", \"none\", otherwise an integer value). [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1GeneMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['accessions'] = \ accessions headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_metadata_by_accession_endpoint.call_with_http_info(**kwargs) def gene_metadata_by_id( self, gene_ids, **kwargs ): """Get gene metadata by GeneID # noqa: E501 Get detailed gene metadata by GeneID in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_metadata_by_id(gene_ids, async_req=True) >>> result = thread.get() Args: gene_ids ([int]): NCBI gene ids Keyword Args: returned_content (V1GeneDatasetRequestContentType): Return either gene-ids, or entire gene metadata. [optional] sort_schema_field (V1GeneDatasetRequestSortField): Select a field to sort on.. [optional] sort_schema_direction (V1SortDirection): Select a direction for the sort.. [optional] limit (str): Limit the number of returned results (\"all\", \"none\", otherwise an integer value). [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1GeneMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['gene_ids'] = \ gene_ids headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_metadata_by_id_endpoint.call_with_http_info(**kwargs) def gene_metadata_by_post( self, v1_gene_dataset_request, **kwargs ): """Get gene metadata as JSON # noqa: E501 Get detailed gene metadata in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_metadata_by_post(v1_gene_dataset_request, async_req=True) >>> result = thread.get() Args: v1_gene_dataset_request (V1GeneDatasetRequest): Keyword Args: _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1GeneMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_gene_dataset_request'] = \ v1_gene_dataset_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_metadata_by_post_endpoint.call_with_http_info(**kwargs) def gene_metadata_by_tax_and_symbol( self, symbols, taxon, **kwargs ): """Get gene metadata by gene symbol # noqa: E501 Get detailed gene metadata by gene symbol in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_metadata_by_tax_and_symbol(symbols, taxon, async_req=True) >>> result = thread.get() Args: symbols ([str]): Gene symbol taxon (str): Taxon for provided gene symbol Keyword Args: accessions ([str]): RNA or Protein accessions.. [optional] returned_content (V1GeneDatasetRequestContentType): Return either gene-ids, or entire gene metadata. [optional] sort_schema_field (V1GeneDatasetRequestSortField): Select a field to sort on.. [optional] sort_schema_direction (V1SortDirection): Select a direction for the sort.. [optional] limit (str): Limit the number of returned results (\"all\", \"none\", otherwise an integer value). [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1GeneMetadata If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['symbols'] = \ symbols kwargs['taxon'] = \ taxon headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_metadata_by_tax_and_symbol_endpoint.call_with_http_info(**kwargs) def gene_metadata_stream_by_post( self, v1_gene_dataset_request, **kwargs ): """Get gene metadata # noqa: E501 Get detailed gene metadata in a streaming, JSON-lines output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_metadata_stream_by_post(v1_gene_dataset_request, async_req=True) >>> result = thread.get() Args: v1_gene_dataset_request (V1GeneDatasetRequest): Keyword Args: _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1GeneMatch If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['v1_gene_dataset_request'] = \ v1_gene_dataset_request headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_metadata_stream_by_post_endpoint.call_with_http_info(**kwargs) def gene_orthologs_by_id( self, gene_id, **kwargs ): """Get gene orthologs by gene ID # noqa: E501 Get detailed gene metadata for an ortholog set by gene ID in a JSON output format. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_orthologs_by_id(gene_id, async_req=True) >>> result = thread.get() Args: gene_id (int): Keyword Args: returned_content (V1OrthologRequestContentType): Return either gene-ids, or entire gene metadata. [optional] taxon_filter ([str]): Filter genes by taxa. [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1OrthologSet If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['gene_id'] = \ gene_id headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_orthologs_by_id_endpoint.call_with_http_info(**kwargs) def gene_tax_name_query( self, taxon_query, **kwargs ): """Get a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name # noqa: E501 This endpoint retrieves a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name of any rank. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_tax_name_query(taxon_query, async_req=True) >>> result = thread.get() Args: taxon_query (str): NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank Keyword Args: tax_rank_filter (V1OrganismQueryRequestTaxRankFilter): Set the scope of searched tax ranks. [optional] tax_resource_filter (V1OrganismQueryRequestTaxonResourceFilter): [optional] _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1SciNameAndIds If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['taxon_query'] = \ taxon_query headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_tax_name_query_endpoint.call_with_http_info(**kwargs) def gene_tax_tree( self, taxon, **kwargs ): """Get a taxonomic subtree by taxonomic identifier # noqa: E501 Using an NCBI Taxonomy ID or name (common or scientific) at any rank, get a subtree filtered for species with assembled genomes. # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.gene_tax_tree(taxon, async_req=True) >>> result = thread.get() Args: taxon (str): NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank Keyword Args: children_only (bool): Only report the children of the requested taxon and not their descendants. [optional] if omitted the server will use the default value of False _return_http_data_only (bool): response data without head status code and headers. Default is True. _preload_content (bool): if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True. _request_timeout (int/float/tuple): timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of (connection, read) timeouts. Default is None. _check_input_type (bool): specifies if type checking should be done one the data sent to the server. Default is True. _check_return_type (bool): specifies if type checking should be done one the data received from the server. Default is True. _host_index (int/None): specifies the index of the server that we want to use. Default is read from the configuration. async_req (bool): execute request asynchronously Returns: V1Organism If the method is called asynchronously, returns the request thread. """ kwargs['async_req'] = kwargs.get( 'async_req', False ) kwargs['_return_http_data_only'] = kwargs.get( '_return_http_data_only', True ) kwargs['_preload_content'] = kwargs.get( '_preload_content', True ) kwargs['_request_timeout'] = kwargs.get( '_request_timeout', None ) kwargs['_check_input_type'] = kwargs.get( '_check_input_type', True ) kwargs['_check_return_type'] = kwargs.get( '_check_return_type', True ) kwargs['_host_index'] = kwargs.get('_host_index') kwargs['taxon'] = \ taxon headers = kwargs.get('headers', {}) if headers: accept = headers.get('accept') or headers.get('Accept') if accept and accept in self.gene_download_summary_by_accession_endpoint.headers_map: self.gene_download_summary_by_accession_endpoint.headers_map['accept'] = accept for key in headers.keys(): self.gene_download_summary_by_accession_endpoint.headers_map[key] = headers[key] return self.gene_tax_tree_endpoint.call_with_http_info(**kwargs)