Bases: object

sars2_protein_download(proteins, **kwargs)¶

Download SARS-CoV-2 protein and CDS datasets by protein name

Download a SARS-CoV-2 protein datasets This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.sars2_protein_download(proteins, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• proteins (list[str]) – Which proteins to retrieve in the data package (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date and time. April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• filename (str) – Output file name.

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

file If the method is called asynchronously, returns the request thread.

sars2_protein_download_with_http_info(proteins, **kwargs)¶

Download SARS-CoV-2 protein and CDS datasets by protein name

Download a SARS-CoV-2 protein datasets This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.sars2_protein_download_with_http_info(proteins, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• proteins (list[str]) – Which proteins to retrieve in the data package (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date and time. April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• filename (str) – Output file name.

• _return_http_data_only – response data without head status code and headers

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

tuple(file, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.

sars2_protein_summary(proteins, **kwargs)¶

Summary of SARS-CoV-2 protein and CDS datasets by protein name

Download a summary of available SARS-CoV-2 protein datasets This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.sars2_protein_summary(proteins, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• proteins (list[str]) – Which proteins to retrieve in the data package (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date and time. April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

V1alpha1DownloadSummary If the method is called asynchronously, returns the request thread.

sars2_protein_summary_with_http_info(proteins, **kwargs)¶

Summary of SARS-CoV-2 protein and CDS datasets by protein name

Download a summary of available SARS-CoV-2 protein datasets This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.sars2_protein_summary_with_http_info(proteins, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• proteins (list[str]) – Which proteins to retrieve in the data package (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date and time. April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• _return_http_data_only – response data without head status code and headers

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

tuple(V1alpha1DownloadSummary, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.

sars2_protein_table(proteins, **kwargs)¶

Get SARS-CoV-2 protein metadata in a tabular format.

Get protein metadata in tabular format for SARS-CoV-2 genomes. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.sars2_protein_table(proteins, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• proteins (list[str]) – Which proteins to retrieve in the data package (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date and time. April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• table_fields (list[str]) – Specify which fields to include in the tabular report.

• format (str) – Choose download format.

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

StreamResultOfV1alpha1TabularOutput If the method is called asynchronously, returns the request thread.

sars2_protein_table_with_http_info(proteins, **kwargs)¶

Get SARS-CoV-2 protein metadata in a tabular format.

Get protein metadata in tabular format for SARS-CoV-2 genomes. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.sars2_protein_table_with_http_info(proteins, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• proteins (list[str]) – Which proteins to retrieve in the data package (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date and time. April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• table_fields (list[str]) – Specify which fields to include in the tabular report.

• format (str) – Choose download format.

• _return_http_data_only – response data without head status code and headers

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

tuple(StreamResultOfV1alpha1TabularOutput, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.

virus_genome_download(taxon, **kwargs)¶

Download Coronavirus genome datasets by taxon

Download a Coronavirus genome datasets by taxon This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.virus_genome_download(taxon, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• pangolin_classification (str) – If set, limit results to genomes classified to this lineage by the PangoLearn tool.

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• exclude_sequence (bool) – Set to true to omit the genomic sequence.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• filename (str) – Output file name.

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

file If the method is called asynchronously, returns the request thread.

virus_genome_download_with_http_info(taxon, **kwargs)¶

Download Coronavirus genome datasets by taxon

Download a Coronavirus genome datasets by taxon This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.virus_genome_download_with_http_info(taxon, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• pangolin_classification (str) – If set, limit results to genomes classified to this lineage by the PangoLearn tool.

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• exclude_sequence (bool) – Set to true to omit the genomic sequence.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• filename (str) – Output file name.

• _return_http_data_only – response data without head status code and headers

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

tuple(file, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.

virus_genome_summary(taxon, **kwargs)¶

Get summary data for Coronaviridae genomes by taxon

Get summary data and download by command line instructions for Coronaviridae genomes by taxon. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.virus_genome_summary(taxon, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• pangolin_classification (str) – If set, limit results to genomes classified to this lineage by the PangoLearn tool.

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• exclude_sequence (bool) – Set to true to omit the genomic sequence.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

V1alpha1DownloadSummary If the method is called asynchronously, returns the request thread.

virus_genome_summary_with_http_info(taxon, **kwargs)¶

Get summary data for Coronaviridae genomes by taxon

Get summary data and download by command line instructions for Coronaviridae genomes by taxon. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.virus_genome_summary_with_http_info(taxon, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• pangolin_classification (str) – If set, limit results to genomes classified to this lineage by the PangoLearn tool.

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• exclude_sequence (bool) – Set to true to omit the genomic sequence.

• include_annotation_type (list[str]) – Select additional types of annotation to include in the data package. If unset, no annotation is provided.

• _return_http_data_only – response data without head status code and headers

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

tuple(V1alpha1DownloadSummary, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.

virus_genome_table(taxon, **kwargs)¶

Get viral genomic metadata in a tabular format.

Get viral genomic metadata in tabular format for Coronaviridae genomes by taxon. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.virus_genome_table(taxon, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• pangolin_classification (str) – If set, limit results to genomes classified to this lineage by the PangoLearn tool.

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• table_fields (list[str]) – Specify which fields to include in the tabular report.

• format (str) – Choose download format (tsv, csv or jsonl).

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

StreamResultOfV1alpha1TabularOutput If the method is called asynchronously, returns the request thread.

virus_genome_table_with_http_info(taxon, **kwargs)¶

Get viral genomic metadata in a tabular format.

Get viral genomic metadata in tabular format for Coronaviridae genomes by taxon. This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True:

thread = api.virus_genome_table_with_http_info(taxon, async_req=True)
result = thread.get()

Parameters

• bool (async_req) – execute request asynchronously

• taxon (str) – NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)

• refseq_only (bool) – If true, limit results to RefSeq genomes.

• annotated_only (bool) – If true, limit results to annotated genomes.

• released_since (datetime) – If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as follows: 2020-04-01T00:00:00.000Z.

• host (str) – If set, limit results to genomes extracted from this host (Taxonomy ID or name).

• pangolin_classification (str) – If set, limit results to genomes classified to this lineage by the PangoLearn tool.

• geo_location (str) – Assemblies from this location (country and state, or continent).

• complete_only (bool) – only include complete genomes.

• table_fields (list[str]) – Specify which fields to include in the tabular report.

• format (str) – Choose download format (tsv, csv or jsonl).

• _return_http_data_only – response data without head status code and headers

• _preload_content – if False, the urllib3.HTTPResponse object will be returned without reading/decoding response data. Default is True.

• _request_timeout – 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.

Returns

tuple(StreamResultOfV1alpha1TabularOutput, status_code(int), headers(HTTPHeaderDict)) If the method is called asynchronously, returns the request thread.