ncbi-datasets-pyclient 18.4.0__py3-none-any.whl → 18.13.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- ncbi/datasets/openapi/__init__.py +603 -250
- ncbi/datasets/openapi/api/bio_sample_api.py +1 -2
- ncbi/datasets/openapi/api/gene_api.py +1331 -1011
- ncbi/datasets/openapi/api/genome_api.py +1129 -1303
- ncbi/datasets/openapi/api/organelle_api.py +1 -2
- ncbi/datasets/openapi/api/prokaryote_api.py +31 -32
- ncbi/datasets/openapi/api/taxonomy_api.py +105 -106
- ncbi/datasets/openapi/api/version_api.py +1 -2
- ncbi/datasets/openapi/api/virus_api.py +772 -830
- ncbi/datasets/openapi/api_client.py +14 -8
- ncbi/datasets/openapi/configuration.py +8 -9
- ncbi/datasets/openapi/exceptions.py +1 -2
- ncbi/datasets/openapi/models/__init__.py +53 -3
- ncbi/datasets/openapi/models/ncbiprotddv2_chain_footprint.py +93 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_query_structure_definition.py +97 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_redundancy_level.py +39 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_sdid_request.py +87 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_similar_structure_report.py +121 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_similar_structure_report_page.py +99 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_similar_structure_request.py +97 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_sort_by_id.py +51 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report.py +141 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_biounit_chain.py +94 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_experiment.py +89 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_kind.py +42 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_ligand_chain.py +94 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_structure_request.py +89 -0
- ncbi/datasets/openapi/models/ncbiprotddv2_vast_score.py +95 -0
- ncbi/datasets/openapi/models/protobuf_any.py +1 -2
- ncbi/datasets/openapi/models/rpc_status.py +1 -2
- ncbi/datasets/openapi/models/v2_accessions.py +87 -0
- ncbi/datasets/openapi/models/v2_annotation_for_assembly_type.py +2 -3
- ncbi/datasets/openapi/models/v2_annotation_for_organelle_type.py +2 -2
- ncbi/datasets/openapi/models/v2_assembly_accessions.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_check_m_histogram_reply.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_check_m_histogram_reply_histogram_interval.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_check_m_histogram_request.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_data_report_draft_request.py +87 -0
- ncbi/datasets/openapi/models/v2_assembly_dataset_availability.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter.py +9 -10
- ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_assembly_source.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_assembly_version.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_metagenome_derived_filter.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_type_material_category.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_dataset_reports_request.py +5 -6
- ncbi/datasets/openapi/models/v2_assembly_dataset_reports_request_content_type.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_dataset_request.py +3 -4
- ncbi/datasets/openapi/models/v2_assembly_dataset_request_resolution.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_links_reply.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_links_reply_assembly_link.py +3 -4
- ncbi/datasets/openapi/models/v2_assembly_links_reply_assembly_link_type.py +3 -3
- ncbi/datasets/openapi/models/v2_assembly_links_request.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_revision_history.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_revision_history_request.py +1 -2
- ncbi/datasets/openapi/models/v2_assembly_sequence_reports_request.py +3 -4
- ncbi/datasets/openapi/models/v2_bio_sample_dataset_reports_request.py +87 -0
- ncbi/datasets/openapi/models/v2_catalog_api_version.py +38 -0
- ncbi/datasets/openapi/models/v2_dataset_request.py +1 -2
- ncbi/datasets/openapi/models/v2_download_summary.py +1 -2
- ncbi/datasets/openapi/models/v2_download_summary_available_files.py +1 -2
- ncbi/datasets/openapi/models/v2_download_summary_dehydrated.py +1 -2
- ncbi/datasets/openapi/models/v2_download_summary_file_summary.py +1 -2
- ncbi/datasets/openapi/models/v2_download_summary_hydrated.py +1 -2
- ncbi/datasets/openapi/models/v2_element_flank_config.py +87 -0
- ncbi/datasets/openapi/models/v2_fasta.py +1 -2
- ncbi/datasets/openapi/models/v2_file_file_type.py +57 -0
- ncbi/datasets/openapi/models/v2_gene_chromosome_summary_reply.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_chromosome_summary_reply_gene_chromosome_summary.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_chromosome_summary_request.py +89 -0
- ncbi/datasets/openapi/models/v2_gene_counts_by_taxon_reply.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_counts_by_taxon_reply_gene_type_and_count.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_counts_by_taxon_request.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_dataset_reports_request.py +20 -9
- ncbi/datasets/openapi/models/v2_gene_dataset_reports_request_content_type.py +1 -3
- ncbi/datasets/openapi/models/v2_gene_dataset_reports_request_symbols_for_taxon.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_dataset_request.py +5 -6
- ncbi/datasets/openapi/models/v2_gene_dataset_request_content_type.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_dataset_request_gene_dataset_report_type.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_links_reply.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_links_reply_gene_link.py +3 -4
- ncbi/datasets/openapi/models/v2_gene_links_reply_gene_link_type.py +2 -2
- ncbi/datasets/openapi/models/v2_gene_links_request.py +1 -2
- ncbi/datasets/openapi/models/v2_gene_pubmed_ids_request.py +87 -0
- ncbi/datasets/openapi/models/v2_gene_pubmed_ids_response.py +87 -0
- ncbi/datasets/openapi/models/v2_gene_type.py +1 -2
- ncbi/datasets/openapi/models/v2_genome_annotation_request.py +5 -6
- ncbi/datasets/openapi/models/v2_genome_annotation_request_annotation_type.py +2 -2
- ncbi/datasets/openapi/models/v2_genome_annotation_request_genome_annotation_table_format.py +1 -2
- ncbi/datasets/openapi/models/v2_genome_annotation_table_summary_reply.py +1 -2
- ncbi/datasets/openapi/models/v2_http_body.py +1 -2
- ncbi/datasets/openapi/models/v2_image_size.py +1 -2
- ncbi/datasets/openapi/models/v2_include_tabular_header.py +1 -2
- ncbi/datasets/openapi/models/v2_micro_bigge_dataset_request.py +96 -0
- ncbi/datasets/openapi/models/v2_micro_bigge_dataset_request_file_type.py +39 -0
- ncbi/datasets/openapi/models/v2_mol_type.py +40 -0
- ncbi/datasets/openapi/models/v2_organelle_download_request.py +1 -2
- ncbi/datasets/openapi/models/v2_organelle_metadata_request.py +7 -8
- ncbi/datasets/openapi/models/v2_organelle_metadata_request_content_type.py +1 -2
- ncbi/datasets/openapi/models/v2_organelle_metadata_request_organelle_table_format.py +1 -2
- ncbi/datasets/openapi/models/v2_organelle_sort.py +3 -4
- ncbi/datasets/openapi/models/v2_organism_query_request.py +5 -6
- ncbi/datasets/openapi/models/v2_organism_query_request_tax_rank_filter.py +1 -2
- ncbi/datasets/openapi/models/v2_organism_query_request_taxon_resource_filter.py +1 -2
- ncbi/datasets/openapi/models/v2_ortholog_request.py +3 -4
- ncbi/datasets/openapi/models/v2_ortholog_request_content_type.py +1 -2
- ncbi/datasets/openapi/models/v2_prokaryote_gene_request.py +1 -2
- ncbi/datasets/openapi/models/v2_prokaryote_gene_request_gene_flank_config.py +1 -2
- ncbi/datasets/openapi/models/v2_ref_gene_catalog_dataset_request.py +96 -0
- ncbi/datasets/openapi/models/v2_ref_gene_catalog_dataset_request_file_type.py +38 -0
- ncbi/datasets/openapi/models/v2_sars2_protein_dataset_request.py +3 -4
- ncbi/datasets/openapi/models/v2_sci_name_and_ids.py +1 -2
- ncbi/datasets/openapi/models/v2_sci_name_and_ids_sci_name_and_id.py +3 -4
- ncbi/datasets/openapi/models/v2_seq_range.py +94 -0
- ncbi/datasets/openapi/models/v2_seq_reply.py +96 -0
- ncbi/datasets/openapi/models/v2_sequence_accession_request.py +1 -2
- ncbi/datasets/openapi/models/v2_sequence_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2_sleep_reply.py +87 -0
- ncbi/datasets/openapi/models/v2_sleep_request.py +89 -0
- ncbi/datasets/openapi/models/v2_sort_direction.py +1 -2
- ncbi/datasets/openapi/models/v2_sort_field.py +3 -4
- ncbi/datasets/openapi/models/v2_table_format.py +1 -2
- ncbi/datasets/openapi/models/v2_tabular_output.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_dataset_request.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_dataset_request_taxonomy_report_type.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_request.py +5 -4
- ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response_edge.py +3 -4
- ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response_edge_child_status.py +2 -2
- ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response_edges_entry.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_image_metadata_request.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_image_metadata_response.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_image_request.py +3 -4
- ncbi/datasets/openapi/models/v2_taxonomy_links_request.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_links_response.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_links_response_generic_link.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_match.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_metadata_request.py +7 -8
- ncbi/datasets/openapi/models/v2_taxonomy_metadata_request_content_type.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_metadata_request_table_format.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_metadata_response.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_node.py +3 -4
- ncbi/datasets/openapi/models/v2_taxonomy_node_count_by_type.py +3 -4
- ncbi/datasets/openapi/models/v2_taxonomy_related_id_request.py +1 -2
- ncbi/datasets/openapi/models/v2_taxonomy_tax_ids_page.py +1 -2
- ncbi/datasets/openapi/models/v2_version_reply.py +1 -2
- ncbi/datasets/openapi/models/v2_viral_sequence_type.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_annotation_filter.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_annotation_report_request.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_availability.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_availability_request.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_data_report_request.py +3 -4
- ncbi/datasets/openapi/models/v2_virus_data_report_request_content_type.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_dataset_filter.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_dataset_report_type.py +1 -2
- ncbi/datasets/openapi/models/v2_virus_dataset_request.py +3 -4
- ncbi/datasets/openapi/models/v2_virus_table_field.py +1 -2
- ncbi/datasets/openapi/models/v2archive_affiliation.py +95 -0
- ncbi/datasets/openapi/models/v2archive_catalog.py +121 -0
- ncbi/datasets/openapi/models/v2archive_location.py +95 -0
- ncbi/datasets/openapi/models/v2archive_modifier.py +90 -0
- ncbi/datasets/openapi/models/v2archive_molecule_type.py +43 -0
- ncbi/datasets/openapi/models/v2archive_name.py +105 -0
- ncbi/datasets/openapi/models/v2archive_nuccore_request.py +87 -0
- ncbi/datasets/openapi/models/v2archive_sequence.py +90 -0
- ncbi/datasets/openapi/models/v2archive_sequence_length_units.py +39 -0
- ncbi/datasets/openapi/models/v2archive_submitter.py +105 -0
- ncbi/datasets/openapi/models/v2archive_taxonomy_node.py +118 -0
- ncbi/datasets/openapi/models/v2archive_taxonomy_subtype.py +77 -0
- ncbi/datasets/openapi/models/v2reports_additional_submitter.py +1 -2
- ncbi/datasets/openapi/models/v2reports_ani_match.py +3 -4
- ncbi/datasets/openapi/models/v2reports_ani_type_category.py +2 -3
- ncbi/datasets/openapi/models/v2reports_annotation.py +1 -2
- ncbi/datasets/openapi/models/v2reports_annotation_info.py +1 -2
- ncbi/datasets/openapi/models/v2reports_assembly_data_report.py +3 -4
- ncbi/datasets/openapi/models/v2reports_assembly_data_report_page.py +3 -4
- ncbi/datasets/openapi/models/v2reports_assembly_info.py +5 -6
- ncbi/datasets/openapi/models/v2reports_assembly_level.py +1 -2
- ncbi/datasets/openapi/models/v2reports_assembly_revision.py +8 -7
- ncbi/datasets/openapi/models/v2reports_assembly_stats.py +4 -3
- ncbi/datasets/openapi/models/v2reports_assembly_status.py +1 -2
- ncbi/datasets/openapi/models/v2reports_atypical_info.py +1 -2
- ncbi/datasets/openapi/models/v2reports_average_nucleotide_identity.py +7 -8
- ncbi/datasets/openapi/models/v2reports_average_nucleotide_identity_match_status.py +1 -2
- ncbi/datasets/openapi/models/v2reports_average_nucleotide_identity_taxonomy_check_status.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_project.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_project_lineage.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_attribute.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_contact.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_data_report.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_data_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_description.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_descriptor.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_id.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_owner.py +1 -2
- ncbi/datasets/openapi/models/v2reports_bio_sample_status.py +1 -2
- ncbi/datasets/openapi/models/v2reports_busco_stat.py +1 -2
- ncbi/datasets/openapi/models/v2reports_check_m.py +1 -2
- ncbi/datasets/openapi/models/v2reports_classification.py +8 -4
- ncbi/datasets/openapi/models/v2reports_collection_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_conserved_domain.py +1 -2
- ncbi/datasets/openapi/models/v2reports_content_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_count_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_error.py +11 -12
- ncbi/datasets/openapi/models/v2reports_error_assembly_error_code.py +1 -2
- ncbi/datasets/openapi/models/v2reports_error_gene_error_code.py +1 -2
- ncbi/datasets/openapi/models/v2reports_error_organelle_error_code.py +1 -2
- ncbi/datasets/openapi/models/v2reports_error_taxonomy_error_code.py +1 -2
- ncbi/datasets/openapi/models/v2reports_error_virus_error_code.py +1 -2
- ncbi/datasets/openapi/models/v2reports_feature_counts.py +1 -2
- ncbi/datasets/openapi/models/v2reports_functional_site.py +97 -0
- ncbi/datasets/openapi/models/v2reports_gene_counts.py +1 -2
- ncbi/datasets/openapi/models/v2reports_gene_data_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2reports_gene_descriptor.py +7 -8
- ncbi/datasets/openapi/models/v2reports_gene_group.py +1 -2
- ncbi/datasets/openapi/models/v2reports_gene_ontology.py +1 -2
- ncbi/datasets/openapi/models/v2reports_gene_report_match.py +1 -2
- ncbi/datasets/openapi/models/v2reports_gene_summary.py +1 -2
- ncbi/datasets/openapi/models/v2reports_gene_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_genome_annotation.py +7 -8
- ncbi/datasets/openapi/models/v2reports_genome_annotation_report_match.py +1 -2
- ncbi/datasets/openapi/models/v2reports_genome_annotation_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2reports_genomic_location.py +1 -2
- ncbi/datasets/openapi/models/v2reports_genomic_region.py +3 -4
- ncbi/datasets/openapi/models/v2reports_genomic_region_genomic_region_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_infraspecific_names.py +1 -2
- ncbi/datasets/openapi/models/v2reports_isolate.py +1 -2
- ncbi/datasets/openapi/models/v2reports_lineage_organism.py +1 -2
- ncbi/datasets/openapi/models/v2reports_linked_assembly.py +3 -4
- ncbi/datasets/openapi/models/v2reports_linked_assembly_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_mature_peptide.py +1 -2
- ncbi/datasets/openapi/models/v2reports_message.py +1 -2
- ncbi/datasets/openapi/models/v2reports_name_and_authority.py +1 -2
- ncbi/datasets/openapi/models/v2reports_name_and_authority_note.py +3 -4
- ncbi/datasets/openapi/models/v2reports_name_and_authority_note_classifier.py +1 -2
- ncbi/datasets/openapi/models/v2reports_name_and_authority_publication.py +1 -2
- ncbi/datasets/openapi/models/v2reports_nomenclature_authority.py +1 -2
- ncbi/datasets/openapi/models/v2reports_organelle.py +5 -6
- ncbi/datasets/openapi/models/v2reports_organelle_biosample.py +1 -2
- ncbi/datasets/openapi/models/v2reports_organelle_data_reports.py +1 -2
- ncbi/datasets/openapi/models/v2reports_organelle_gene_counts.py +1 -2
- ncbi/datasets/openapi/models/v2reports_organelle_info.py +1 -2
- ncbi/datasets/openapi/models/v2reports_organelle_topology.py +1 -2
- ncbi/datasets/openapi/models/v2reports_organelle_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_organism.py +1 -2
- ncbi/datasets/openapi/models/v2reports_orientation.py +1 -2
- ncbi/datasets/openapi/models/v2reports_paired_assembly.py +7 -6
- ncbi/datasets/openapi/models/v2reports_process_metadata.py +1 -2
- ncbi/datasets/openapi/models/v2reports_product_descriptor.py +5 -6
- ncbi/datasets/openapi/models/v2reports_prokaryote_gene_location_completeness.py +37 -0
- ncbi/datasets/openapi/models/v2reports_protein.py +1 -2
- ncbi/datasets/openapi/models/v2reports_protein_conserved_domain.py +103 -0
- ncbi/datasets/openapi/models/v2reports_protein_data_report.py +127 -0
- ncbi/datasets/openapi/models/v2reports_protein_data_report_page.py +95 -0
- ncbi/datasets/openapi/models/v2reports_protein_family.py +95 -0
- ncbi/datasets/openapi/models/v2reports_purpose_of_sampling.py +1 -2
- ncbi/datasets/openapi/models/v2reports_range.py +3 -4
- ncbi/datasets/openapi/models/v2reports_rank_type.py +3 -2
- ncbi/datasets/openapi/models/v2reports_reference.py +1 -2
- ncbi/datasets/openapi/models/v2reports_rna_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_seq_range_set.py +1 -2
- ncbi/datasets/openapi/models/v2reports_seq_range_set_fasta.py +1 -2
- ncbi/datasets/openapi/models/v2reports_sequence_info.py +1 -2
- ncbi/datasets/openapi/models/v2reports_sequence_information.py +1 -2
- ncbi/datasets/openapi/models/v2reports_source_database.py +1 -2
- ncbi/datasets/openapi/models/v2reports_tax_data.py +1 -2
- ncbi/datasets/openapi/models/v2reports_taxonomy_data_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2reports_taxonomy_names_data_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2reports_taxonomy_names_descriptor.py +3 -4
- ncbi/datasets/openapi/models/v2reports_taxonomy_names_descriptor_citation.py +1 -2
- ncbi/datasets/openapi/models/v2reports_taxonomy_names_report_match.py +1 -2
- ncbi/datasets/openapi/models/v2reports_taxonomy_node.py +7 -6
- ncbi/datasets/openapi/models/v2reports_taxonomy_node_count_by_type.py +3 -4
- ncbi/datasets/openapi/models/v2reports_taxonomy_report_match.py +1 -2
- ncbi/datasets/openapi/models/v2reports_taxonomy_type_material.py +1 -2
- ncbi/datasets/openapi/models/v2reports_transcript.py +5 -6
- ncbi/datasets/openapi/models/v2reports_transcript_select_category.py +1 -2
- ncbi/datasets/openapi/models/v2reports_transcript_transcript_type.py +1 -2
- ncbi/datasets/openapi/models/v2reports_transcript_type_count.py +3 -4
- ncbi/datasets/openapi/models/v2reports_type_material.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_annotation_report.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_annotation_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_assembly.py +5 -6
- ncbi/datasets/openapi/models/v2reports_virus_assembly_collection_location.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_assembly_completeness.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_assembly_submitter_info.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_data_report_page.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_gene.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_peptide.py +3 -4
- ncbi/datasets/openapi/models/v2reports_virus_peptide_uni_prot_id.py +1 -2
- ncbi/datasets/openapi/models/v2reports_virus_peptide_viral_peptide_completeness.py +1 -2
- ncbi/datasets/openapi/models/v2reports_warning.py +3 -4
- ncbi/datasets/openapi/models/v2reports_warning_gene_warning_code.py +1 -2
- ncbi/datasets/openapi/models/v2reports_warning_replaced_id.py +1 -2
- ncbi/datasets/openapi/models/v2reports_wgs_info.py +1 -2
- ncbi/datasets/openapi/rest.py +1 -2
- ncbi_datasets_pyclient-18.13.0.dist-info/METADATA +537 -0
- ncbi_datasets_pyclient-18.13.0.dist-info/RECORD +305 -0
- ncbi_datasets_pyclient-18.4.0.dist-info/METADATA +0 -25
- ncbi_datasets_pyclient-18.4.0.dist-info/RECORD +0 -254
- {ncbi_datasets_pyclient-18.4.0.dist-info → ncbi_datasets_pyclient-18.13.0.dist-info}/WHEEL +0 -0
- {ncbi_datasets_pyclient-18.4.0.dist-info → ncbi_datasets_pyclient-18.13.0.dist-info}/licenses/LICENSE +0 -0
- {ncbi_datasets_pyclient-18.4.0.dist-info → ncbi_datasets_pyclient-18.13.0.dist-info}/top_level.txt +0 -0
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### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is
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The version of the OpenAPI document: v2
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Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report by protein name.
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:param released_since:
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:param updated_since:
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:param pangolin_classification:
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:param geo_location:
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:param usa_state:
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:param complete_only:
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:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
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:param include_sequence: Specify which sequence files to include in the
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:param aux_report:
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:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
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) -> bytearray:
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"""
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"""Get a SARS-CoV-2 protein data package
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Download SARS-CoV-2 protein
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Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report.
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:type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
|
|
@@ -631,9 +630,9 @@ class VirusApi:
|
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) -> ApiResponse[bytearray]:
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-
"""
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+
"""Get a SARS-CoV-2 protein data package
|
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|
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|
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|
-
Download SARS-CoV-2 protein
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+
Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report.
|
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:param v2_sars2_protein_dataset_request: (required)
|
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:type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
|
|
@@ -702,9 +701,9 @@ class VirusApi:
|
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|
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) -> RESTResponseType:
|
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|
-
"""
|
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|
+
"""Get a SARS-CoV-2 protein data package
|
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|
|
|
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|
-
Download SARS-CoV-2 protein
|
|
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|
+
Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report.
|
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|
|
|
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:param v2_sars2_protein_dataset_request: (required)
|
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:type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
|
|
@@ -837,18 +836,18 @@ class VirusApi:
|
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|
@validate_call
|
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|
def sars2_protein_summary(
|
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|
self,
|
|
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|
-
proteins: Annotated[List[StrictStr], Field(description="
|
|
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|
+
proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
|
|
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|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
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|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
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|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
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|
-
updated_since: Optional[datetime] = None,
|
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|
-
host: Annotated[Optional[StrictStr], Field(description="
|
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|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
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|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
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|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
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|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
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|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the
|
|
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|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
842
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
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|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
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|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
845
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
|
|
846
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
847
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
848
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
849
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
850
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
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|
_request_timeout: Union[
|
|
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|
None,
|
|
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853
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -862,33 +861,33 @@ class VirusApi:
|
|
|
862
861
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
863
862
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
864
863
|
) -> V2DownloadSummary:
|
|
865
|
-
"""
|
|
864
|
+
"""Get a download summary of a SARS-CoV-2 protein data package by protein name
|
|
866
865
|
|
|
867
|
-
|
|
866
|
+
Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
|
|
868
867
|
|
|
869
|
-
:param proteins:
|
|
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|
+
:param proteins: One or more SARS-CoV-2 protein names (required)
|
|
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|
:type proteins: List[str]
|
|
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870
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
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|
:type refseq_only: bool
|
|
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|
:param annotated_only: If true, limit results to annotated genomes.
|
|
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|
:type annotated_only: bool
|
|
875
|
-
:param released_since:
|
|
874
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
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875
|
:type released_since: datetime
|
|
877
|
-
:param updated_since:
|
|
876
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
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877
|
:type updated_since: datetime
|
|
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|
-
:param host:
|
|
878
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
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879
|
:type host: str
|
|
881
|
-
:param pangolin_classification:
|
|
880
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
|
|
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881
|
:type pangolin_classification: str
|
|
883
|
-
:param geo_location:
|
|
882
|
+
:param geo_location: Limit to genomes collected from the specififed geographic location.
|
|
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883
|
:type geo_location: str
|
|
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|
-
:param usa_state:
|
|
884
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
886
885
|
:type usa_state: str
|
|
887
|
-
:param complete_only:
|
|
886
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
888
887
|
:type complete_only: bool
|
|
889
|
-
:param include_sequence: Specify which sequence files to include in the
|
|
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|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
890
889
|
:type include_sequence: List[V2ViralSequenceType]
|
|
891
|
-
:param aux_report:
|
|
890
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
892
891
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
893
892
|
:param _request_timeout: timeout setting for this request. If one
|
|
894
893
|
number provided, it will be total request
|
|
@@ -948,18 +947,18 @@ class VirusApi:
|
|
|
948
947
|
@validate_call
|
|
949
948
|
def sars2_protein_summary_with_http_info(
|
|
950
949
|
self,
|
|
951
|
-
proteins: Annotated[List[StrictStr], Field(description="
|
|
950
|
+
proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
|
|
952
951
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
953
952
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
954
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
955
|
-
updated_since: Optional[datetime] = None,
|
|
956
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
957
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
958
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
959
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
960
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
961
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the
|
|
962
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
953
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
954
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
955
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
956
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
|
|
957
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
958
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
959
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
960
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
961
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
963
962
|
_request_timeout: Union[
|
|
964
963
|
None,
|
|
965
964
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -973,33 +972,33 @@ class VirusApi:
|
|
|
973
972
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
974
973
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
975
974
|
) -> ApiResponse[V2DownloadSummary]:
|
|
976
|
-
"""
|
|
975
|
+
"""Get a download summary of a SARS-CoV-2 protein data package by protein name
|
|
977
976
|
|
|
978
|
-
|
|
977
|
+
Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
|
|
979
978
|
|
|
980
|
-
:param proteins:
|
|
979
|
+
:param proteins: One or more SARS-CoV-2 protein names (required)
|
|
981
980
|
:type proteins: List[str]
|
|
982
981
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
983
982
|
:type refseq_only: bool
|
|
984
983
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
985
984
|
:type annotated_only: bool
|
|
986
|
-
:param released_since:
|
|
985
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
987
986
|
:type released_since: datetime
|
|
988
|
-
:param updated_since:
|
|
987
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
989
988
|
:type updated_since: datetime
|
|
990
|
-
:param host:
|
|
989
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
991
990
|
:type host: str
|
|
992
|
-
:param pangolin_classification:
|
|
991
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
|
|
993
992
|
:type pangolin_classification: str
|
|
994
|
-
:param geo_location:
|
|
993
|
+
:param geo_location: Limit to genomes collected from the specififed geographic location.
|
|
995
994
|
:type geo_location: str
|
|
996
|
-
:param usa_state:
|
|
995
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
997
996
|
:type usa_state: str
|
|
998
|
-
:param complete_only:
|
|
997
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
999
998
|
:type complete_only: bool
|
|
1000
|
-
:param include_sequence: Specify which sequence files to include in the
|
|
999
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
1001
1000
|
:type include_sequence: List[V2ViralSequenceType]
|
|
1002
|
-
:param aux_report:
|
|
1001
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
1003
1002
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
1004
1003
|
:param _request_timeout: timeout setting for this request. If one
|
|
1005
1004
|
number provided, it will be total request
|
|
@@ -1059,18 +1058,18 @@ class VirusApi:
|
|
|
1059
1058
|
@validate_call
|
|
1060
1059
|
def sars2_protein_summary_without_preload_content(
|
|
1061
1060
|
self,
|
|
1062
|
-
proteins: Annotated[List[StrictStr], Field(description="
|
|
1061
|
+
proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
|
|
1063
1062
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
1064
1063
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
1065
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
1066
|
-
updated_since: Optional[datetime] = None,
|
|
1067
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
1068
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
1069
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
1070
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
1071
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
1072
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the
|
|
1073
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
1064
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
1065
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
1066
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
1067
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
|
|
1068
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
1069
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
1070
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
1071
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
1072
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
1074
1073
|
_request_timeout: Union[
|
|
1075
1074
|
None,
|
|
1076
1075
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -1084,33 +1083,33 @@ class VirusApi:
|
|
|
1084
1083
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
1085
1084
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
1086
1085
|
) -> RESTResponseType:
|
|
1087
|
-
"""
|
|
1086
|
+
"""Get a download summary of a SARS-CoV-2 protein data package by protein name
|
|
1088
1087
|
|
|
1089
|
-
|
|
1088
|
+
Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
|
|
1090
1089
|
|
|
1091
|
-
:param proteins:
|
|
1090
|
+
:param proteins: One or more SARS-CoV-2 protein names (required)
|
|
1092
1091
|
:type proteins: List[str]
|
|
1093
1092
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
1094
1093
|
:type refseq_only: bool
|
|
1095
1094
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
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1095
|
:type annotated_only: bool
|
|
1097
|
-
:param released_since:
|
|
1096
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
1098
1097
|
:type released_since: datetime
|
|
1099
|
-
:param updated_since:
|
|
1098
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
1100
1099
|
:type updated_since: datetime
|
|
1101
|
-
:param host:
|
|
1100
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
1102
1101
|
:type host: str
|
|
1103
|
-
:param pangolin_classification:
|
|
1102
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
|
|
1104
1103
|
:type pangolin_classification: str
|
|
1105
|
-
:param geo_location:
|
|
1104
|
+
:param geo_location: Limit to genomes collected from the specififed geographic location.
|
|
1106
1105
|
:type geo_location: str
|
|
1107
|
-
:param usa_state:
|
|
1106
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
1108
1107
|
:type usa_state: str
|
|
1109
|
-
:param complete_only:
|
|
1108
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
1110
1109
|
:type complete_only: bool
|
|
1111
|
-
:param include_sequence: Specify which sequence files to include in the
|
|
1110
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
1112
1111
|
:type include_sequence: List[V2ViralSequenceType]
|
|
1113
|
-
:param aux_report:
|
|
1112
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
1114
1113
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
1115
1114
|
:param _request_timeout: timeout setting for this request. If one
|
|
1116
1115
|
number provided, it will be total request
|
|
@@ -1321,9 +1320,9 @@ class VirusApi:
|
|
|
1321
1320
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
1322
1321
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
1323
1322
|
) -> V2DownloadSummary:
|
|
1324
|
-
"""
|
|
1323
|
+
"""Get a download summary of a SARS-CoV-2 protein data package by protein name
|
|
1325
1324
|
|
|
1326
|
-
|
|
1325
|
+
Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
|
|
1327
1326
|
|
|
1328
1327
|
:param v2_sars2_protein_dataset_request: (required)
|
|
1329
1328
|
:type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
|
|
@@ -1388,9 +1387,9 @@ class VirusApi:
|
|
|
1388
1387
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
1389
1388
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
1390
1389
|
) -> ApiResponse[V2DownloadSummary]:
|
|
1391
|
-
"""
|
|
1390
|
+
"""Get a download summary of a SARS-CoV-2 protein data package by protein name
|
|
1392
1391
|
|
|
1393
|
-
|
|
1392
|
+
Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
|
|
1394
1393
|
|
|
1395
1394
|
:param v2_sars2_protein_dataset_request: (required)
|
|
1396
1395
|
:type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
|
|
@@ -1455,9 +1454,9 @@ class VirusApi:
|
|
|
1455
1454
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
1456
1455
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
1457
1456
|
) -> RESTResponseType:
|
|
1458
|
-
"""
|
|
1457
|
+
"""Get a download summary of a SARS-CoV-2 protein data package by protein name
|
|
1459
1458
|
|
|
1460
|
-
|
|
1459
|
+
Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
|
|
1461
1460
|
|
|
1462
1461
|
:param v2_sars2_protein_dataset_request: (required)
|
|
1463
1462
|
:type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
|
|
@@ -1582,20 +1581,18 @@ class VirusApi:
|
|
|
1582
1581
|
@validate_call
|
|
1583
1582
|
def sars2_protein_table(
|
|
1584
1583
|
self,
|
|
1585
|
-
proteins: Annotated[List[StrictStr], Field(description="
|
|
1584
|
+
proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
|
|
1586
1585
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
1587
1586
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
1588
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
1589
|
-
updated_since: Optional[datetime] = None,
|
|
1590
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
1591
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
1592
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
1593
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
1594
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
1587
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
1588
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
1589
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
1590
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
|
|
1591
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
1592
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
1593
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
1595
1594
|
table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
1596
|
-
|
|
1597
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
|
|
1598
|
-
format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
|
|
1595
|
+
format: Annotated[Optional[V2TableFormat], Field(description="Specify output format")] = None,
|
|
1599
1596
|
_request_timeout: Union[
|
|
1600
1597
|
None,
|
|
1601
1598
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -1609,37 +1606,33 @@ class VirusApi:
|
|
|
1609
1606
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
1610
1607
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
1611
1608
|
) -> V2TabularOutput:
|
|
1612
|
-
"""Get SARS-CoV-2 protein metadata in a tabular format
|
|
1609
|
+
"""Get SARS-CoV-2 protein metadata in a tabular format by protein name
|
|
1613
1610
|
|
|
1614
|
-
Get protein metadata in tabular format
|
|
1611
|
+
Get SARS-CoV-2 protein metadata in a tabular format by protein name.
|
|
1615
1612
|
|
|
1616
|
-
:param proteins:
|
|
1613
|
+
:param proteins: One or more SARS-CoV-2 protein names (required)
|
|
1617
1614
|
:type proteins: List[str]
|
|
1618
1615
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
1619
1616
|
:type refseq_only: bool
|
|
1620
1617
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
1621
1618
|
:type annotated_only: bool
|
|
1622
|
-
:param released_since:
|
|
1619
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
1623
1620
|
:type released_since: datetime
|
|
1624
|
-
:param updated_since:
|
|
1621
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
1625
1622
|
:type updated_since: datetime
|
|
1626
|
-
:param host:
|
|
1623
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
1627
1624
|
:type host: str
|
|
1628
|
-
:param pangolin_classification:
|
|
1625
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
|
|
1629
1626
|
:type pangolin_classification: str
|
|
1630
|
-
:param geo_location:
|
|
1627
|
+
:param geo_location: Limit to genomes collected from the specififed geographic location.
|
|
1631
1628
|
:type geo_location: str
|
|
1632
|
-
:param usa_state:
|
|
1629
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
1633
1630
|
:type usa_state: str
|
|
1634
|
-
:param complete_only:
|
|
1631
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
1635
1632
|
:type complete_only: bool
|
|
1636
1633
|
:param table_fields: Specify which fields to include in the tabular report
|
|
1637
1634
|
:type table_fields: List[V2VirusTableField]
|
|
1638
|
-
:param
|
|
1639
|
-
:type include_sequence: List[V2ViralSequenceType]
|
|
1640
|
-
:param aux_report: List additional reports to include with download. Data report is included by default.
|
|
1641
|
-
:type aux_report: List[V2VirusDatasetReportType]
|
|
1642
|
-
:param format: Choose download format (tsv, csv or jsonl)
|
|
1635
|
+
:param format: Specify output format
|
|
1643
1636
|
:type format: V2TableFormat
|
|
1644
1637
|
:param _request_timeout: timeout setting for this request. If one
|
|
1645
1638
|
number provided, it will be total request
|
|
@@ -1675,8 +1668,6 @@ class VirusApi:
|
|
|
1675
1668
|
usa_state=usa_state,
|
|
1676
1669
|
complete_only=complete_only,
|
|
1677
1670
|
table_fields=table_fields,
|
|
1678
|
-
include_sequence=include_sequence,
|
|
1679
|
-
aux_report=aux_report,
|
|
1680
1671
|
format=format,
|
|
1681
1672
|
_request_auth=_request_auth,
|
|
1682
1673
|
_content_type=_content_type,
|
|
@@ -1701,20 +1692,18 @@ class VirusApi:
|
|
|
1701
1692
|
@validate_call
|
|
1702
1693
|
def sars2_protein_table_with_http_info(
|
|
1703
1694
|
self,
|
|
1704
|
-
proteins: Annotated[List[StrictStr], Field(description="
|
|
1695
|
+
proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
|
|
1705
1696
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
1706
1697
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
1707
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
1708
|
-
updated_since: Optional[datetime] = None,
|
|
1709
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
1710
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
1711
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
1712
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
1713
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
1698
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
1699
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
1700
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
1701
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
|
|
1702
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
1703
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
1704
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
1714
1705
|
table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
1715
|
-
|
|
1716
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
|
|
1717
|
-
format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
|
|
1706
|
+
format: Annotated[Optional[V2TableFormat], Field(description="Specify output format")] = None,
|
|
1718
1707
|
_request_timeout: Union[
|
|
1719
1708
|
None,
|
|
1720
1709
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -1728,37 +1717,33 @@ class VirusApi:
|
|
|
1728
1717
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
1729
1718
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
1730
1719
|
) -> ApiResponse[V2TabularOutput]:
|
|
1731
|
-
"""Get SARS-CoV-2 protein metadata in a tabular format
|
|
1720
|
+
"""Get SARS-CoV-2 protein metadata in a tabular format by protein name
|
|
1732
1721
|
|
|
1733
|
-
Get protein metadata in tabular format
|
|
1722
|
+
Get SARS-CoV-2 protein metadata in a tabular format by protein name.
|
|
1734
1723
|
|
|
1735
|
-
:param proteins:
|
|
1724
|
+
:param proteins: One or more SARS-CoV-2 protein names (required)
|
|
1736
1725
|
:type proteins: List[str]
|
|
1737
1726
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
1738
1727
|
:type refseq_only: bool
|
|
1739
1728
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
1740
1729
|
:type annotated_only: bool
|
|
1741
|
-
:param released_since:
|
|
1730
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
1742
1731
|
:type released_since: datetime
|
|
1743
|
-
:param updated_since:
|
|
1732
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
1744
1733
|
:type updated_since: datetime
|
|
1745
|
-
:param host:
|
|
1734
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
1746
1735
|
:type host: str
|
|
1747
|
-
:param pangolin_classification:
|
|
1736
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
|
|
1748
1737
|
:type pangolin_classification: str
|
|
1749
|
-
:param geo_location:
|
|
1738
|
+
:param geo_location: Limit to genomes collected from the specififed geographic location.
|
|
1750
1739
|
:type geo_location: str
|
|
1751
|
-
:param usa_state:
|
|
1740
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
1752
1741
|
:type usa_state: str
|
|
1753
|
-
:param complete_only:
|
|
1742
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
1754
1743
|
:type complete_only: bool
|
|
1755
1744
|
:param table_fields: Specify which fields to include in the tabular report
|
|
1756
1745
|
:type table_fields: List[V2VirusTableField]
|
|
1757
|
-
:param
|
|
1758
|
-
:type include_sequence: List[V2ViralSequenceType]
|
|
1759
|
-
:param aux_report: List additional reports to include with download. Data report is included by default.
|
|
1760
|
-
:type aux_report: List[V2VirusDatasetReportType]
|
|
1761
|
-
:param format: Choose download format (tsv, csv or jsonl)
|
|
1746
|
+
:param format: Specify output format
|
|
1762
1747
|
:type format: V2TableFormat
|
|
1763
1748
|
:param _request_timeout: timeout setting for this request. If one
|
|
1764
1749
|
number provided, it will be total request
|
|
@@ -1794,8 +1779,6 @@ class VirusApi:
|
|
|
1794
1779
|
usa_state=usa_state,
|
|
1795
1780
|
complete_only=complete_only,
|
|
1796
1781
|
table_fields=table_fields,
|
|
1797
|
-
include_sequence=include_sequence,
|
|
1798
|
-
aux_report=aux_report,
|
|
1799
1782
|
format=format,
|
|
1800
1783
|
_request_auth=_request_auth,
|
|
1801
1784
|
_content_type=_content_type,
|
|
@@ -1820,20 +1803,18 @@ class VirusApi:
|
|
|
1820
1803
|
@validate_call
|
|
1821
1804
|
def sars2_protein_table_without_preload_content(
|
|
1822
1805
|
self,
|
|
1823
|
-
proteins: Annotated[List[StrictStr], Field(description="
|
|
1806
|
+
proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
|
|
1824
1807
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
1825
1808
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
1826
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
1827
|
-
updated_since: Optional[datetime] = None,
|
|
1828
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
1829
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
1830
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
1831
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
1832
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
1809
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
1810
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
1811
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
1812
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
|
|
1813
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
1814
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
1815
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
1833
1816
|
table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
1834
|
-
|
|
1835
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
|
|
1836
|
-
format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
|
|
1817
|
+
format: Annotated[Optional[V2TableFormat], Field(description="Specify output format")] = None,
|
|
1837
1818
|
_request_timeout: Union[
|
|
1838
1819
|
None,
|
|
1839
1820
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -1847,37 +1828,33 @@ class VirusApi:
|
|
|
1847
1828
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
1848
1829
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
1849
1830
|
) -> RESTResponseType:
|
|
1850
|
-
"""Get SARS-CoV-2 protein metadata in a tabular format
|
|
1831
|
+
"""Get SARS-CoV-2 protein metadata in a tabular format by protein name
|
|
1851
1832
|
|
|
1852
|
-
Get protein metadata in tabular format
|
|
1833
|
+
Get SARS-CoV-2 protein metadata in a tabular format by protein name.
|
|
1853
1834
|
|
|
1854
|
-
:param proteins:
|
|
1835
|
+
:param proteins: One or more SARS-CoV-2 protein names (required)
|
|
1855
1836
|
:type proteins: List[str]
|
|
1856
1837
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
1857
1838
|
:type refseq_only: bool
|
|
1858
1839
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
1859
1840
|
:type annotated_only: bool
|
|
1860
|
-
:param released_since:
|
|
1841
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
1861
1842
|
:type released_since: datetime
|
|
1862
|
-
:param updated_since:
|
|
1843
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
1863
1844
|
:type updated_since: datetime
|
|
1864
|
-
:param host:
|
|
1845
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
1865
1846
|
:type host: str
|
|
1866
|
-
:param pangolin_classification:
|
|
1847
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
|
|
1867
1848
|
:type pangolin_classification: str
|
|
1868
|
-
:param geo_location:
|
|
1849
|
+
:param geo_location: Limit to genomes collected from the specififed geographic location.
|
|
1869
1850
|
:type geo_location: str
|
|
1870
|
-
:param usa_state:
|
|
1851
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
1871
1852
|
:type usa_state: str
|
|
1872
|
-
:param complete_only:
|
|
1853
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
1873
1854
|
:type complete_only: bool
|
|
1874
1855
|
:param table_fields: Specify which fields to include in the tabular report
|
|
1875
1856
|
:type table_fields: List[V2VirusTableField]
|
|
1876
|
-
:param
|
|
1877
|
-
:type include_sequence: List[V2ViralSequenceType]
|
|
1878
|
-
:param aux_report: List additional reports to include with download. Data report is included by default.
|
|
1879
|
-
:type aux_report: List[V2VirusDatasetReportType]
|
|
1880
|
-
:param format: Choose download format (tsv, csv or jsonl)
|
|
1857
|
+
:param format: Specify output format
|
|
1881
1858
|
:type format: V2TableFormat
|
|
1882
1859
|
:param _request_timeout: timeout setting for this request. If one
|
|
1883
1860
|
number provided, it will be total request
|
|
@@ -1913,8 +1890,6 @@ class VirusApi:
|
|
|
1913
1890
|
usa_state=usa_state,
|
|
1914
1891
|
complete_only=complete_only,
|
|
1915
1892
|
table_fields=table_fields,
|
|
1916
|
-
include_sequence=include_sequence,
|
|
1917
|
-
aux_report=aux_report,
|
|
1918
1893
|
format=format,
|
|
1919
1894
|
_request_auth=_request_auth,
|
|
1920
1895
|
_content_type=_content_type,
|
|
@@ -1945,8 +1920,6 @@ class VirusApi:
|
|
|
1945
1920
|
usa_state,
|
|
1946
1921
|
complete_only,
|
|
1947
1922
|
table_fields,
|
|
1948
|
-
include_sequence,
|
|
1949
|
-
aux_report,
|
|
1950
1923
|
format,
|
|
1951
1924
|
_request_auth,
|
|
1952
1925
|
_content_type,
|
|
@@ -1959,8 +1932,6 @@ class VirusApi:
|
|
|
1959
1932
|
_collection_formats: Dict[str, str] = {
|
|
1960
1933
|
'proteins': 'csv',
|
|
1961
1934
|
'table_fields': 'multi',
|
|
1962
|
-
'include_sequence': 'multi',
|
|
1963
|
-
'aux_report': 'multi',
|
|
1964
1935
|
}
|
|
1965
1936
|
|
|
1966
1937
|
_path_params: Dict[str, str] = {}
|
|
@@ -2034,14 +2005,6 @@ class VirusApi:
|
|
|
2034
2005
|
|
|
2035
2006
|
_query_params.append(('table_fields', table_fields))
|
|
2036
2007
|
|
|
2037
|
-
if include_sequence is not None:
|
|
2038
|
-
|
|
2039
|
-
_query_params.append(('include_sequence', include_sequence))
|
|
2040
|
-
|
|
2041
|
-
if aux_report is not None:
|
|
2042
|
-
|
|
2043
|
-
_query_params.append(('aux_report', aux_report))
|
|
2044
|
-
|
|
2045
2008
|
if format is not None:
|
|
2046
2009
|
|
|
2047
2010
|
_query_params.append(('format', format.value))
|
|
@@ -2101,9 +2064,9 @@ class VirusApi:
|
|
|
2101
2064
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2102
2065
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2103
2066
|
) -> V2VirusAvailability:
|
|
2104
|
-
"""Check
|
|
2067
|
+
"""Check the validity of a virus genome nucleotide accession
|
|
2105
2068
|
|
|
2106
|
-
Check
|
|
2069
|
+
Check the validity of a virus genome nucleotide accession. Output in JSON format.
|
|
2107
2070
|
|
|
2108
2071
|
:param accessions: virus accessions (required)
|
|
2109
2072
|
:type accessions: List[str]
|
|
@@ -2168,9 +2131,9 @@ class VirusApi:
|
|
|
2168
2131
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2169
2132
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2170
2133
|
) -> ApiResponse[V2VirusAvailability]:
|
|
2171
|
-
"""Check
|
|
2134
|
+
"""Check the validity of a virus genome nucleotide accession
|
|
2172
2135
|
|
|
2173
|
-
Check
|
|
2136
|
+
Check the validity of a virus genome nucleotide accession. Output in JSON format.
|
|
2174
2137
|
|
|
2175
2138
|
:param accessions: virus accessions (required)
|
|
2176
2139
|
:type accessions: List[str]
|
|
@@ -2235,9 +2198,9 @@ class VirusApi:
|
|
|
2235
2198
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2236
2199
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2237
2200
|
) -> RESTResponseType:
|
|
2238
|
-
"""Check
|
|
2201
|
+
"""Check the validity of a virus genome nucleotide accession
|
|
2239
2202
|
|
|
2240
|
-
Check
|
|
2203
|
+
Check the validity of a virus genome nucleotide accession. Output in JSON format.
|
|
2241
2204
|
|
|
2242
2205
|
:param accessions: virus accessions (required)
|
|
2243
2206
|
:type accessions: List[str]
|
|
@@ -2364,9 +2327,9 @@ class VirusApi:
|
|
|
2364
2327
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2365
2328
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2366
2329
|
) -> V2VirusAvailability:
|
|
2367
|
-
"""Check
|
|
2330
|
+
"""Check the validity of a virus genome nucleotide accession
|
|
2368
2331
|
|
|
2369
|
-
Check
|
|
2332
|
+
Check the validity of a virus genome nucleotide accession. Output in JSON format.
|
|
2370
2333
|
|
|
2371
2334
|
:param v2_virus_availability_request: (required)
|
|
2372
2335
|
:type v2_virus_availability_request: V2VirusAvailabilityRequest
|
|
@@ -2431,9 +2394,9 @@ class VirusApi:
|
|
|
2431
2394
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2432
2395
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2433
2396
|
) -> ApiResponse[V2VirusAvailability]:
|
|
2434
|
-
"""Check
|
|
2397
|
+
"""Check the validity of a virus genome nucleotide accession
|
|
2435
2398
|
|
|
2436
|
-
Check
|
|
2399
|
+
Check the validity of a virus genome nucleotide accession. Output in JSON format.
|
|
2437
2400
|
|
|
2438
2401
|
:param v2_virus_availability_request: (required)
|
|
2439
2402
|
:type v2_virus_availability_request: V2VirusAvailabilityRequest
|
|
@@ -2498,9 +2461,9 @@ class VirusApi:
|
|
|
2498
2461
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2499
2462
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2500
2463
|
) -> RESTResponseType:
|
|
2501
|
-
"""Check
|
|
2464
|
+
"""Check the validity of a virus genome nucleotide accession
|
|
2502
2465
|
|
|
2503
|
-
Check
|
|
2466
|
+
Check the validity of a virus genome nucleotide accession. Output in JSON format.
|
|
2504
2467
|
|
|
2505
2468
|
:param v2_virus_availability_request: (required)
|
|
2506
2469
|
:type v2_virus_availability_request: V2VirusAvailabilityRequest
|
|
@@ -2625,19 +2588,19 @@ class VirusApi:
|
|
|
2625
2588
|
@validate_call
|
|
2626
2589
|
def virus_annotation_reports_by_acessions(
|
|
2627
2590
|
self,
|
|
2628
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
2629
|
-
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
2630
|
-
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
2631
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
2632
|
-
filter_updated_since: Optional[datetime] = None,
|
|
2633
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
2634
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
2635
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
2636
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
2637
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
2638
|
-
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
2591
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
2592
|
+
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
|
|
2593
|
+
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
|
|
2594
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
2595
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
2596
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
2597
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
2598
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
2599
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
2600
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
2601
|
+
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
|
|
2639
2602
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
2640
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
2603
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
2641
2604
|
_request_timeout: Union[
|
|
2642
2605
|
None,
|
|
2643
2606
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -2651,35 +2614,35 @@ class VirusApi:
|
|
|
2651
2614
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2652
2615
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2653
2616
|
) -> V2reportsVirusAnnotationReportPage:
|
|
2654
|
-
"""Get virus annotation report by accession
|
|
2617
|
+
"""Get a virus annotation report by nucleotide accession
|
|
2655
2618
|
|
|
2656
|
-
Get virus annotation report by accesion. By default, in paged JSON format, but also available
|
|
2619
|
+
Get a virus annotation report by nucleotide accesion. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
2657
2620
|
|
|
2658
|
-
:param accessions:
|
|
2621
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
2659
2622
|
:type accessions: List[str]
|
|
2660
|
-
:param filter_refseq_only: If true, limit
|
|
2623
|
+
:param filter_refseq_only: If true, limit to RefSeq genomes.
|
|
2661
2624
|
:type filter_refseq_only: bool
|
|
2662
|
-
:param filter_annotated_only: If true, limit
|
|
2625
|
+
:param filter_annotated_only: If true, limit to annotated genomes.
|
|
2663
2626
|
:type filter_annotated_only: bool
|
|
2664
|
-
:param filter_released_since:
|
|
2627
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
2665
2628
|
:type filter_released_since: datetime
|
|
2666
|
-
:param filter_updated_since:
|
|
2629
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
2667
2630
|
:type filter_updated_since: datetime
|
|
2668
|
-
:param filter_host:
|
|
2631
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
2669
2632
|
:type filter_host: str
|
|
2670
|
-
:param filter_pangolin_classification:
|
|
2633
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
2671
2634
|
:type filter_pangolin_classification: str
|
|
2672
|
-
:param filter_geo_location:
|
|
2635
|
+
:param filter_geo_location: Limit to genomes collected from the specififed geographic location.
|
|
2673
2636
|
:type filter_geo_location: str
|
|
2674
|
-
:param filter_usa_state:
|
|
2637
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
2675
2638
|
:type filter_usa_state: str
|
|
2676
|
-
:param filter_complete_only:
|
|
2639
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
2677
2640
|
:type filter_complete_only: bool
|
|
2678
|
-
:param table_fields: Specify which fields to include in the tabular report
|
|
2641
|
+
:param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
|
|
2679
2642
|
:type table_fields: List[str]
|
|
2680
2643
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
2681
2644
|
:type page_size: int
|
|
2682
|
-
:param page_token: A page token is returned
|
|
2645
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
2683
2646
|
:type page_token: str
|
|
2684
2647
|
:param _request_timeout: timeout setting for this request. If one
|
|
2685
2648
|
number provided, it will be total request
|
|
@@ -2740,19 +2703,19 @@ class VirusApi:
|
|
|
2740
2703
|
@validate_call
|
|
2741
2704
|
def virus_annotation_reports_by_acessions_with_http_info(
|
|
2742
2705
|
self,
|
|
2743
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
2744
|
-
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
2745
|
-
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
2746
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
2747
|
-
filter_updated_since: Optional[datetime] = None,
|
|
2748
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
2749
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
2750
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
2751
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
2752
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
2753
|
-
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
2706
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
2707
|
+
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
|
|
2708
|
+
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
|
|
2709
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
2710
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
2711
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
2712
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
2713
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
2714
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
2715
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
2716
|
+
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
|
|
2754
2717
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
2755
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
2718
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
2756
2719
|
_request_timeout: Union[
|
|
2757
2720
|
None,
|
|
2758
2721
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -2766,35 +2729,35 @@ class VirusApi:
|
|
|
2766
2729
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2767
2730
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2768
2731
|
) -> ApiResponse[V2reportsVirusAnnotationReportPage]:
|
|
2769
|
-
"""Get virus annotation report by accession
|
|
2732
|
+
"""Get a virus annotation report by nucleotide accession
|
|
2770
2733
|
|
|
2771
|
-
Get virus annotation report by accesion. By default, in paged JSON format, but also available
|
|
2734
|
+
Get a virus annotation report by nucleotide accesion. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
2772
2735
|
|
|
2773
|
-
:param accessions:
|
|
2736
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
2774
2737
|
:type accessions: List[str]
|
|
2775
|
-
:param filter_refseq_only: If true, limit
|
|
2738
|
+
:param filter_refseq_only: If true, limit to RefSeq genomes.
|
|
2776
2739
|
:type filter_refseq_only: bool
|
|
2777
|
-
:param filter_annotated_only: If true, limit
|
|
2740
|
+
:param filter_annotated_only: If true, limit to annotated genomes.
|
|
2778
2741
|
:type filter_annotated_only: bool
|
|
2779
|
-
:param filter_released_since:
|
|
2742
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
2780
2743
|
:type filter_released_since: datetime
|
|
2781
|
-
:param filter_updated_since:
|
|
2744
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
2782
2745
|
:type filter_updated_since: datetime
|
|
2783
|
-
:param filter_host:
|
|
2746
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
2784
2747
|
:type filter_host: str
|
|
2785
|
-
:param filter_pangolin_classification:
|
|
2748
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
2786
2749
|
:type filter_pangolin_classification: str
|
|
2787
|
-
:param filter_geo_location:
|
|
2750
|
+
:param filter_geo_location: Limit to genomes collected from the specififed geographic location.
|
|
2788
2751
|
:type filter_geo_location: str
|
|
2789
|
-
:param filter_usa_state:
|
|
2752
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
2790
2753
|
:type filter_usa_state: str
|
|
2791
|
-
:param filter_complete_only:
|
|
2754
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
2792
2755
|
:type filter_complete_only: bool
|
|
2793
|
-
:param table_fields: Specify which fields to include in the tabular report
|
|
2756
|
+
:param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
|
|
2794
2757
|
:type table_fields: List[str]
|
|
2795
2758
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
2796
2759
|
:type page_size: int
|
|
2797
|
-
:param page_token: A page token is returned
|
|
2760
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
2798
2761
|
:type page_token: str
|
|
2799
2762
|
:param _request_timeout: timeout setting for this request. If one
|
|
2800
2763
|
number provided, it will be total request
|
|
@@ -2855,19 +2818,19 @@ class VirusApi:
|
|
|
2855
2818
|
@validate_call
|
|
2856
2819
|
def virus_annotation_reports_by_acessions_without_preload_content(
|
|
2857
2820
|
self,
|
|
2858
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
2859
|
-
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
2860
|
-
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
2861
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
2862
|
-
filter_updated_since: Optional[datetime] = None,
|
|
2863
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
2864
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
2865
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
2866
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
2867
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
2868
|
-
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
2821
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
2822
|
+
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
|
|
2823
|
+
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
|
|
2824
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
2825
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
2826
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
2827
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
2828
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
2829
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
2830
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
2831
|
+
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
|
|
2869
2832
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
2870
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
2833
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
2871
2834
|
_request_timeout: Union[
|
|
2872
2835
|
None,
|
|
2873
2836
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -2881,35 +2844,35 @@ class VirusApi:
|
|
|
2881
2844
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
2882
2845
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
2883
2846
|
) -> RESTResponseType:
|
|
2884
|
-
"""Get virus annotation report by accession
|
|
2847
|
+
"""Get a virus annotation report by nucleotide accession
|
|
2885
2848
|
|
|
2886
|
-
Get virus annotation report by accesion. By default, in paged JSON format, but also available
|
|
2849
|
+
Get a virus annotation report by nucleotide accesion. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
2887
2850
|
|
|
2888
|
-
:param accessions:
|
|
2851
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
2889
2852
|
:type accessions: List[str]
|
|
2890
|
-
:param filter_refseq_only: If true, limit
|
|
2853
|
+
:param filter_refseq_only: If true, limit to RefSeq genomes.
|
|
2891
2854
|
:type filter_refseq_only: bool
|
|
2892
|
-
:param filter_annotated_only: If true, limit
|
|
2855
|
+
:param filter_annotated_only: If true, limit to annotated genomes.
|
|
2893
2856
|
:type filter_annotated_only: bool
|
|
2894
|
-
:param filter_released_since:
|
|
2857
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
2895
2858
|
:type filter_released_since: datetime
|
|
2896
|
-
:param filter_updated_since:
|
|
2859
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
2897
2860
|
:type filter_updated_since: datetime
|
|
2898
|
-
:param filter_host:
|
|
2861
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
2899
2862
|
:type filter_host: str
|
|
2900
|
-
:param filter_pangolin_classification:
|
|
2863
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
2901
2864
|
:type filter_pangolin_classification: str
|
|
2902
|
-
:param filter_geo_location:
|
|
2865
|
+
:param filter_geo_location: Limit to genomes collected from the specififed geographic location.
|
|
2903
2866
|
:type filter_geo_location: str
|
|
2904
|
-
:param filter_usa_state:
|
|
2867
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
2905
2868
|
:type filter_usa_state: str
|
|
2906
|
-
:param filter_complete_only:
|
|
2869
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
2907
2870
|
:type filter_complete_only: bool
|
|
2908
|
-
:param table_fields: Specify which fields to include in the tabular report
|
|
2871
|
+
:param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
|
|
2909
2872
|
:type table_fields: List[str]
|
|
2910
2873
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
2911
2874
|
:type page_size: int
|
|
2912
|
-
:param page_token: A page token is returned
|
|
2875
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
2913
2876
|
:type page_token: str
|
|
2914
2877
|
:param _request_timeout: timeout setting for this request. If one
|
|
2915
2878
|
number provided, it will be total request
|
|
@@ -3127,9 +3090,9 @@ class VirusApi:
|
|
|
3127
3090
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
3128
3091
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
3129
3092
|
) -> V2reportsVirusAnnotationReportPage:
|
|
3130
|
-
"""Get virus annotation report
|
|
3093
|
+
"""Get a virus annotation report
|
|
3131
3094
|
|
|
3132
|
-
Get virus annotation report. By default, in paged JSON format, but also available
|
|
3095
|
+
Get a virus annotation report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
3133
3096
|
|
|
3134
3097
|
:param v2_virus_annotation_report_request: (required)
|
|
3135
3098
|
:type v2_virus_annotation_report_request: V2VirusAnnotationReportRequest
|
|
@@ -3194,9 +3157,9 @@ class VirusApi:
|
|
|
3194
3157
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
3195
3158
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
3196
3159
|
) -> ApiResponse[V2reportsVirusAnnotationReportPage]:
|
|
3197
|
-
"""Get virus annotation report
|
|
3160
|
+
"""Get a virus annotation report
|
|
3198
3161
|
|
|
3199
|
-
Get virus annotation report. By default, in paged JSON format, but also available
|
|
3162
|
+
Get a virus annotation report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
3200
3163
|
|
|
3201
3164
|
:param v2_virus_annotation_report_request: (required)
|
|
3202
3165
|
:type v2_virus_annotation_report_request: V2VirusAnnotationReportRequest
|
|
@@ -3261,9 +3224,9 @@ class VirusApi:
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3261
3224
|
_headers: Optional[Dict[StrictStr, Any]] = None,
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3262
3225
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
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3263
3226
|
) -> RESTResponseType:
|
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3264
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-
"""Get virus annotation report
|
|
3227
|
+
"""Get a virus annotation report
|
|
3265
3228
|
|
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3266
|
-
Get virus annotation report. By default, in paged JSON format, but also available
|
|
3229
|
+
Get a virus annotation report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
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3267
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3231
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:param v2_virus_annotation_report_request: (required)
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3269
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:type v2_virus_annotation_report_request: V2VirusAnnotationReportRequest
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@@ -3391,18 +3354,18 @@ class VirusApi:
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3391
3354
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def virus_annotation_reports_by_taxon(
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3392
3355
|
self,
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3393
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taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
3394
|
-
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
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3395
|
-
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
3396
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
3397
|
-
filter_updated_since: Optional[datetime] = None,
|
|
3398
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
3399
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
3400
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
3401
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
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3402
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
3403
|
-
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
3357
|
+
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
|
|
3358
|
+
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
|
|
3359
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
3360
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
3361
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
3362
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
3363
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
3364
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
3365
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
3366
|
+
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
|
|
3404
3367
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
3405
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
3368
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
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3369
|
_request_timeout: Union[
|
|
3407
3370
|
None,
|
|
3408
3371
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -3416,35 +3379,35 @@ class VirusApi:
|
|
|
3416
3379
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
3417
3380
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
3418
3381
|
) -> V2reportsVirusAnnotationReportPage:
|
|
3419
|
-
"""Get virus annotation report by taxon
|
|
3382
|
+
"""Get a virus annotation report by taxon
|
|
3420
3383
|
|
|
3421
|
-
Get virus annotation report by taxon. By default, in paged JSON format, but also available
|
|
3384
|
+
Get virus annotation report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
3422
3385
|
|
|
3423
3386
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
3424
3387
|
:type taxon: str
|
|
3425
|
-
:param filter_refseq_only: If true, limit
|
|
3388
|
+
:param filter_refseq_only: If true, limit to RefSeq genomes.
|
|
3426
3389
|
:type filter_refseq_only: bool
|
|
3427
|
-
:param filter_annotated_only: If true, limit
|
|
3390
|
+
:param filter_annotated_only: If true, limit to annotated genomes.
|
|
3428
3391
|
:type filter_annotated_only: bool
|
|
3429
|
-
:param filter_released_since:
|
|
3392
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
3430
3393
|
:type filter_released_since: datetime
|
|
3431
|
-
:param filter_updated_since:
|
|
3394
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
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3395
|
:type filter_updated_since: datetime
|
|
3433
|
-
:param filter_host:
|
|
3396
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
3434
3397
|
:type filter_host: str
|
|
3435
|
-
:param filter_pangolin_classification:
|
|
3398
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
3436
3399
|
:type filter_pangolin_classification: str
|
|
3437
|
-
:param filter_geo_location:
|
|
3400
|
+
:param filter_geo_location: Limit to genomes collected from the specififed geographic location.
|
|
3438
3401
|
:type filter_geo_location: str
|
|
3439
|
-
:param filter_usa_state:
|
|
3402
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
3440
3403
|
:type filter_usa_state: str
|
|
3441
|
-
:param filter_complete_only:
|
|
3404
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
3442
3405
|
:type filter_complete_only: bool
|
|
3443
|
-
:param table_fields: Specify which fields to include in the tabular report
|
|
3406
|
+
:param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
|
|
3444
3407
|
:type table_fields: List[str]
|
|
3445
3408
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
3446
3409
|
:type page_size: int
|
|
3447
|
-
:param page_token: A page token is returned
|
|
3410
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
3448
3411
|
:type page_token: str
|
|
3449
3412
|
:param _request_timeout: timeout setting for this request. If one
|
|
3450
3413
|
number provided, it will be total request
|
|
@@ -3506,18 +3469,18 @@ class VirusApi:
|
|
|
3506
3469
|
def virus_annotation_reports_by_taxon_with_http_info(
|
|
3507
3470
|
self,
|
|
3508
3471
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
3509
|
-
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
3510
|
-
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
3511
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
3512
|
-
filter_updated_since: Optional[datetime] = None,
|
|
3513
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
3514
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
3515
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
3516
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
3517
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
3518
|
-
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
3472
|
+
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
|
|
3473
|
+
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
|
|
3474
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
3475
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
3476
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
3477
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
3478
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
3479
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
3480
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
3481
|
+
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
|
|
3519
3482
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
3520
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
3483
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
3521
3484
|
_request_timeout: Union[
|
|
3522
3485
|
None,
|
|
3523
3486
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -3531,35 +3494,35 @@ class VirusApi:
|
|
|
3531
3494
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
3532
3495
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
3533
3496
|
) -> ApiResponse[V2reportsVirusAnnotationReportPage]:
|
|
3534
|
-
"""Get virus annotation report by taxon
|
|
3497
|
+
"""Get a virus annotation report by taxon
|
|
3535
3498
|
|
|
3536
|
-
Get virus annotation report by taxon. By default, in paged JSON format, but also available
|
|
3499
|
+
Get virus annotation report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
3537
3500
|
|
|
3538
3501
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
3539
3502
|
:type taxon: str
|
|
3540
|
-
:param filter_refseq_only: If true, limit
|
|
3503
|
+
:param filter_refseq_only: If true, limit to RefSeq genomes.
|
|
3541
3504
|
:type filter_refseq_only: bool
|
|
3542
|
-
:param filter_annotated_only: If true, limit
|
|
3505
|
+
:param filter_annotated_only: If true, limit to annotated genomes.
|
|
3543
3506
|
:type filter_annotated_only: bool
|
|
3544
|
-
:param filter_released_since:
|
|
3507
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
3545
3508
|
:type filter_released_since: datetime
|
|
3546
|
-
:param filter_updated_since:
|
|
3509
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
3547
3510
|
:type filter_updated_since: datetime
|
|
3548
|
-
:param filter_host:
|
|
3511
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
3549
3512
|
:type filter_host: str
|
|
3550
|
-
:param filter_pangolin_classification:
|
|
3513
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
3551
3514
|
:type filter_pangolin_classification: str
|
|
3552
|
-
:param filter_geo_location:
|
|
3515
|
+
:param filter_geo_location: Limit to genomes collected from the specififed geographic location.
|
|
3553
3516
|
:type filter_geo_location: str
|
|
3554
|
-
:param filter_usa_state:
|
|
3517
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
3555
3518
|
:type filter_usa_state: str
|
|
3556
|
-
:param filter_complete_only:
|
|
3519
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
3557
3520
|
:type filter_complete_only: bool
|
|
3558
|
-
:param table_fields: Specify which fields to include in the tabular report
|
|
3521
|
+
:param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
|
|
3559
3522
|
:type table_fields: List[str]
|
|
3560
3523
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
3561
3524
|
:type page_size: int
|
|
3562
|
-
:param page_token: A page token is returned
|
|
3525
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
3563
3526
|
:type page_token: str
|
|
3564
3527
|
:param _request_timeout: timeout setting for this request. If one
|
|
3565
3528
|
number provided, it will be total request
|
|
@@ -3621,18 +3584,18 @@ class VirusApi:
|
|
|
3621
3584
|
def virus_annotation_reports_by_taxon_without_preload_content(
|
|
3622
3585
|
self,
|
|
3623
3586
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
3624
|
-
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
3625
|
-
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit
|
|
3626
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
3627
|
-
filter_updated_since: Optional[datetime] = None,
|
|
3628
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
3629
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
3630
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
3631
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
3632
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
3633
|
-
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
3587
|
+
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
|
|
3588
|
+
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
|
|
3589
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
3590
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
3591
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
3592
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
3593
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
|
|
3594
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
3595
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
3596
|
+
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
|
|
3634
3597
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
3635
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
3598
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
3636
3599
|
_request_timeout: Union[
|
|
3637
3600
|
None,
|
|
3638
3601
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -3646,35 +3609,35 @@ class VirusApi:
|
|
|
3646
3609
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
3647
3610
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
3648
3611
|
) -> RESTResponseType:
|
|
3649
|
-
"""Get virus annotation report by taxon
|
|
3612
|
+
"""Get a virus annotation report by taxon
|
|
3650
3613
|
|
|
3651
|
-
Get virus annotation report by taxon. By default, in paged JSON format, but also available
|
|
3614
|
+
Get virus annotation report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
3652
3615
|
|
|
3653
3616
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
3654
3617
|
:type taxon: str
|
|
3655
|
-
:param filter_refseq_only: If true, limit
|
|
3618
|
+
:param filter_refseq_only: If true, limit to RefSeq genomes.
|
|
3656
3619
|
:type filter_refseq_only: bool
|
|
3657
|
-
:param filter_annotated_only: If true, limit
|
|
3620
|
+
:param filter_annotated_only: If true, limit to annotated genomes.
|
|
3658
3621
|
:type filter_annotated_only: bool
|
|
3659
|
-
:param filter_released_since:
|
|
3622
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
3660
3623
|
:type filter_released_since: datetime
|
|
3661
|
-
:param filter_updated_since:
|
|
3624
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
3662
3625
|
:type filter_updated_since: datetime
|
|
3663
|
-
:param filter_host:
|
|
3626
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
3664
3627
|
:type filter_host: str
|
|
3665
|
-
:param filter_pangolin_classification:
|
|
3628
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
3666
3629
|
:type filter_pangolin_classification: str
|
|
3667
|
-
:param filter_geo_location:
|
|
3630
|
+
:param filter_geo_location: Limit to genomes collected from the specififed geographic location.
|
|
3668
3631
|
:type filter_geo_location: str
|
|
3669
|
-
:param filter_usa_state:
|
|
3632
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
3670
3633
|
:type filter_usa_state: str
|
|
3671
|
-
:param filter_complete_only:
|
|
3634
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
3672
3635
|
:type filter_complete_only: bool
|
|
3673
|
-
:param table_fields: Specify which fields to include in the tabular report
|
|
3636
|
+
:param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
|
|
3674
3637
|
:type table_fields: List[str]
|
|
3675
3638
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
3676
3639
|
:type page_size: int
|
|
3677
|
-
:param page_token: A page token is returned
|
|
3640
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
3678
3641
|
:type page_token: str
|
|
3679
3642
|
:param _request_timeout: timeout setting for this request. If one
|
|
3680
3643
|
number provided, it will be total request
|
|
@@ -3878,18 +3841,17 @@ class VirusApi:
|
|
|
3878
3841
|
def virus_genome_download(
|
|
3879
3842
|
self,
|
|
3880
3843
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
3881
|
-
taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
|
|
3882
3844
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
3883
3845
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
3884
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
3885
|
-
updated_since: Optional[datetime] = None,
|
|
3886
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
3887
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
3888
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
3889
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
3890
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
3891
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
3892
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
3846
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
3847
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
3848
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
3849
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
3850
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
3851
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
3852
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
3853
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
3854
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
3893
3855
|
use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
|
|
3894
3856
|
filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
|
|
3895
3857
|
_request_timeout: Union[
|
|
@@ -3905,35 +3867,33 @@ class VirusApi:
|
|
|
3905
3867
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
3906
3868
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
3907
3869
|
) -> bytearray:
|
|
3908
|
-
"""
|
|
3870
|
+
"""Get a virus genome data package by taxon
|
|
3909
3871
|
|
|
3910
|
-
Download a virus genome
|
|
3872
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.
|
|
3911
3873
|
|
|
3912
3874
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
3913
3875
|
:type taxon: str
|
|
3914
|
-
:param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
|
|
3915
|
-
:type taxons: List[str]
|
|
3916
3876
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
3917
3877
|
:type refseq_only: bool
|
|
3918
3878
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
3919
3879
|
:type annotated_only: bool
|
|
3920
|
-
:param released_since:
|
|
3880
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
3921
3881
|
:type released_since: datetime
|
|
3922
|
-
:param updated_since:
|
|
3882
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
3923
3883
|
:type updated_since: datetime
|
|
3924
|
-
:param host:
|
|
3884
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
3925
3885
|
:type host: str
|
|
3926
|
-
:param pangolin_classification:
|
|
3886
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
3927
3887
|
:type pangolin_classification: str
|
|
3928
|
-
:param geo_location:
|
|
3888
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
3929
3889
|
:type geo_location: str
|
|
3930
|
-
:param usa_state:
|
|
3890
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
3931
3891
|
:type usa_state: str
|
|
3932
|
-
:param complete_only:
|
|
3892
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
3933
3893
|
:type complete_only: bool
|
|
3934
|
-
:param include_sequence:
|
|
3894
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
3935
3895
|
:type include_sequence: List[V2ViralSequenceType]
|
|
3936
|
-
:param aux_report:
|
|
3896
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
3937
3897
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
3938
3898
|
:param use_psg: Experimental approach to retrieving sequence data.
|
|
3939
3899
|
:type use_psg: bool
|
|
@@ -3963,7 +3923,6 @@ class VirusApi:
|
|
|
3963
3923
|
|
|
3964
3924
|
_param = self._virus_genome_download_serialize(
|
|
3965
3925
|
taxon=taxon,
|
|
3966
|
-
taxons=taxons,
|
|
3967
3926
|
refseq_only=refseq_only,
|
|
3968
3927
|
annotated_only=annotated_only,
|
|
3969
3928
|
released_since=released_since,
|
|
@@ -4001,18 +3960,17 @@ class VirusApi:
|
|
|
4001
3960
|
def virus_genome_download_with_http_info(
|
|
4002
3961
|
self,
|
|
4003
3962
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
4004
|
-
taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
|
|
4005
3963
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
4006
3964
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
4007
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
4008
|
-
updated_since: Optional[datetime] = None,
|
|
4009
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
4010
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
4011
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
4012
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
4013
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
4014
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
4015
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
3965
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
3966
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
3967
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
3968
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
3969
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
3970
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
3971
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
3972
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
3973
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
4016
3974
|
use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
|
|
4017
3975
|
filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
|
|
4018
3976
|
_request_timeout: Union[
|
|
@@ -4028,35 +3986,33 @@ class VirusApi:
|
|
|
4028
3986
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
4029
3987
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
4030
3988
|
) -> ApiResponse[bytearray]:
|
|
4031
|
-
"""
|
|
3989
|
+
"""Get a virus genome data package by taxon
|
|
4032
3990
|
|
|
4033
|
-
Download a virus genome
|
|
3991
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.
|
|
4034
3992
|
|
|
4035
3993
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
4036
3994
|
:type taxon: str
|
|
4037
|
-
:param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
|
|
4038
|
-
:type taxons: List[str]
|
|
4039
3995
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
4040
3996
|
:type refseq_only: bool
|
|
4041
3997
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
4042
3998
|
:type annotated_only: bool
|
|
4043
|
-
:param released_since:
|
|
3999
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
4044
4000
|
:type released_since: datetime
|
|
4045
|
-
:param updated_since:
|
|
4001
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
4046
4002
|
:type updated_since: datetime
|
|
4047
|
-
:param host:
|
|
4003
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
4048
4004
|
:type host: str
|
|
4049
|
-
:param pangolin_classification:
|
|
4005
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
4050
4006
|
:type pangolin_classification: str
|
|
4051
|
-
:param geo_location:
|
|
4007
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
4052
4008
|
:type geo_location: str
|
|
4053
|
-
:param usa_state:
|
|
4009
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
4054
4010
|
:type usa_state: str
|
|
4055
|
-
:param complete_only:
|
|
4011
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
4056
4012
|
:type complete_only: bool
|
|
4057
|
-
:param include_sequence:
|
|
4013
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
4058
4014
|
:type include_sequence: List[V2ViralSequenceType]
|
|
4059
|
-
:param aux_report:
|
|
4015
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
4060
4016
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
4061
4017
|
:param use_psg: Experimental approach to retrieving sequence data.
|
|
4062
4018
|
:type use_psg: bool
|
|
@@ -4086,7 +4042,6 @@ class VirusApi:
|
|
|
4086
4042
|
|
|
4087
4043
|
_param = self._virus_genome_download_serialize(
|
|
4088
4044
|
taxon=taxon,
|
|
4089
|
-
taxons=taxons,
|
|
4090
4045
|
refseq_only=refseq_only,
|
|
4091
4046
|
annotated_only=annotated_only,
|
|
4092
4047
|
released_since=released_since,
|
|
@@ -4124,18 +4079,17 @@ class VirusApi:
|
|
|
4124
4079
|
def virus_genome_download_without_preload_content(
|
|
4125
4080
|
self,
|
|
4126
4081
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
4127
|
-
taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
|
|
4128
4082
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
4129
4083
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
4130
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
4131
|
-
updated_since: Optional[datetime] = None,
|
|
4132
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
4133
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
4134
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
4135
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
4136
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
4137
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
4138
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
4084
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
4085
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
4086
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
4087
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
4088
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
4089
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
4090
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
4091
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
4092
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
4139
4093
|
use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
|
|
4140
4094
|
filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
|
|
4141
4095
|
_request_timeout: Union[
|
|
@@ -4151,35 +4105,33 @@ class VirusApi:
|
|
|
4151
4105
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
4152
4106
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
4153
4107
|
) -> RESTResponseType:
|
|
4154
|
-
"""
|
|
4108
|
+
"""Get a virus genome data package by taxon
|
|
4155
4109
|
|
|
4156
|
-
Download a virus genome
|
|
4110
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.
|
|
4157
4111
|
|
|
4158
4112
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
4159
4113
|
:type taxon: str
|
|
4160
|
-
:param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
|
|
4161
|
-
:type taxons: List[str]
|
|
4162
4114
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
4163
4115
|
:type refseq_only: bool
|
|
4164
4116
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
4165
4117
|
:type annotated_only: bool
|
|
4166
|
-
:param released_since:
|
|
4118
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
4167
4119
|
:type released_since: datetime
|
|
4168
|
-
:param updated_since:
|
|
4120
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
4169
4121
|
:type updated_since: datetime
|
|
4170
|
-
:param host:
|
|
4122
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
4171
4123
|
:type host: str
|
|
4172
|
-
:param pangolin_classification:
|
|
4124
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
4173
4125
|
:type pangolin_classification: str
|
|
4174
|
-
:param geo_location:
|
|
4126
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
4175
4127
|
:type geo_location: str
|
|
4176
|
-
:param usa_state:
|
|
4128
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
4177
4129
|
:type usa_state: str
|
|
4178
|
-
:param complete_only:
|
|
4130
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
4179
4131
|
:type complete_only: bool
|
|
4180
|
-
:param include_sequence:
|
|
4132
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
4181
4133
|
:type include_sequence: List[V2ViralSequenceType]
|
|
4182
|
-
:param aux_report:
|
|
4134
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
4183
4135
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
4184
4136
|
:param use_psg: Experimental approach to retrieving sequence data.
|
|
4185
4137
|
:type use_psg: bool
|
|
@@ -4209,7 +4161,6 @@ class VirusApi:
|
|
|
4209
4161
|
|
|
4210
4162
|
_param = self._virus_genome_download_serialize(
|
|
4211
4163
|
taxon=taxon,
|
|
4212
|
-
taxons=taxons,
|
|
4213
4164
|
refseq_only=refseq_only,
|
|
4214
4165
|
annotated_only=annotated_only,
|
|
4215
4166
|
released_since=released_since,
|
|
@@ -4242,7 +4193,6 @@ class VirusApi:
|
|
|
4242
4193
|
def _virus_genome_download_serialize(
|
|
4243
4194
|
self,
|
|
4244
4195
|
taxon,
|
|
4245
|
-
taxons,
|
|
4246
4196
|
refseq_only,
|
|
4247
4197
|
annotated_only,
|
|
4248
4198
|
released_since,
|
|
@@ -4265,7 +4215,6 @@ class VirusApi:
|
|
|
4265
4215
|
_host = None
|
|
4266
4216
|
|
|
4267
4217
|
_collection_formats: Dict[str, str] = {
|
|
4268
|
-
'taxons': 'multi',
|
|
4269
4218
|
'include_sequence': 'multi',
|
|
4270
4219
|
'aux_report': 'multi',
|
|
4271
4220
|
}
|
|
@@ -4283,10 +4232,6 @@ class VirusApi:
|
|
|
4283
4232
|
if taxon is not None:
|
|
4284
4233
|
_path_params['taxon'] = taxon
|
|
4285
4234
|
# process the query parameters
|
|
4286
|
-
if taxons is not None:
|
|
4287
|
-
|
|
4288
|
-
_query_params.append(('taxons', taxons))
|
|
4289
|
-
|
|
4290
4235
|
if refseq_only is not None:
|
|
4291
4236
|
|
|
4292
4237
|
_query_params.append(('refseq_only', refseq_only))
|
|
@@ -4398,19 +4343,19 @@ class VirusApi:
|
|
|
4398
4343
|
@validate_call
|
|
4399
4344
|
def virus_genome_download_accession(
|
|
4400
4345
|
self,
|
|
4401
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
4346
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
4402
4347
|
taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
|
|
4403
4348
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
4404
4349
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
4405
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
4406
|
-
updated_since: Optional[datetime] = None,
|
|
4407
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
4408
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
4409
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
4410
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
4411
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
4412
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
4413
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
4350
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
4351
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
4352
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
4353
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
4354
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
4355
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
4356
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
4357
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
4358
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
4414
4359
|
use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
|
|
4415
4360
|
filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
|
|
4416
4361
|
_request_timeout: Union[
|
|
@@ -4426,11 +4371,11 @@ class VirusApi:
|
|
|
4426
4371
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
4427
4372
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
4428
4373
|
) -> bytearray:
|
|
4429
|
-
"""
|
|
4374
|
+
"""Get a virus genome data package by nucleotide accession
|
|
4430
4375
|
|
|
4431
|
-
Download a virus genome
|
|
4376
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
|
|
4432
4377
|
|
|
4433
|
-
:param accessions:
|
|
4378
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
4434
4379
|
:type accessions: List[str]
|
|
4435
4380
|
:param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
|
|
4436
4381
|
:type taxons: List[str]
|
|
@@ -4438,23 +4383,23 @@ class VirusApi:
|
|
|
4438
4383
|
:type refseq_only: bool
|
|
4439
4384
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
4440
4385
|
:type annotated_only: bool
|
|
4441
|
-
:param released_since:
|
|
4386
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
4442
4387
|
:type released_since: datetime
|
|
4443
|
-
:param updated_since:
|
|
4388
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
4444
4389
|
:type updated_since: datetime
|
|
4445
|
-
:param host:
|
|
4390
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
4446
4391
|
:type host: str
|
|
4447
|
-
:param pangolin_classification:
|
|
4392
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
4448
4393
|
:type pangolin_classification: str
|
|
4449
|
-
:param geo_location:
|
|
4394
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
4450
4395
|
:type geo_location: str
|
|
4451
|
-
:param usa_state:
|
|
4396
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
4452
4397
|
:type usa_state: str
|
|
4453
|
-
:param complete_only:
|
|
4398
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
4454
4399
|
:type complete_only: bool
|
|
4455
|
-
:param include_sequence:
|
|
4400
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
4456
4401
|
:type include_sequence: List[V2ViralSequenceType]
|
|
4457
|
-
:param aux_report:
|
|
4402
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
4458
4403
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
4459
4404
|
:param use_psg: Experimental approach to retrieving sequence data.
|
|
4460
4405
|
:type use_psg: bool
|
|
@@ -4521,19 +4466,19 @@ class VirusApi:
|
|
|
4521
4466
|
@validate_call
|
|
4522
4467
|
def virus_genome_download_accession_with_http_info(
|
|
4523
4468
|
self,
|
|
4524
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
4469
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
4525
4470
|
taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
|
|
4526
4471
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
4527
4472
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
4528
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
4529
|
-
updated_since: Optional[datetime] = None,
|
|
4530
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
4531
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
4532
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
4533
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
4534
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
4535
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
4536
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
4473
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
4474
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
4475
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
4476
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
4477
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
4478
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
4479
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
4480
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
4481
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
4537
4482
|
use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
|
|
4538
4483
|
filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
|
|
4539
4484
|
_request_timeout: Union[
|
|
@@ -4549,11 +4494,11 @@ class VirusApi:
|
|
|
4549
4494
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
4550
4495
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
4551
4496
|
) -> ApiResponse[bytearray]:
|
|
4552
|
-
"""
|
|
4497
|
+
"""Get a virus genome data package by nucleotide accession
|
|
4553
4498
|
|
|
4554
|
-
Download a virus genome
|
|
4499
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
|
|
4555
4500
|
|
|
4556
|
-
:param accessions:
|
|
4501
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
4557
4502
|
:type accessions: List[str]
|
|
4558
4503
|
:param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
|
|
4559
4504
|
:type taxons: List[str]
|
|
@@ -4561,23 +4506,23 @@ class VirusApi:
|
|
|
4561
4506
|
:type refseq_only: bool
|
|
4562
4507
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
4563
4508
|
:type annotated_only: bool
|
|
4564
|
-
:param released_since:
|
|
4509
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
4565
4510
|
:type released_since: datetime
|
|
4566
|
-
:param updated_since:
|
|
4511
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
4567
4512
|
:type updated_since: datetime
|
|
4568
|
-
:param host:
|
|
4513
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
4569
4514
|
:type host: str
|
|
4570
|
-
:param pangolin_classification:
|
|
4515
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
4571
4516
|
:type pangolin_classification: str
|
|
4572
|
-
:param geo_location:
|
|
4517
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
4573
4518
|
:type geo_location: str
|
|
4574
|
-
:param usa_state:
|
|
4519
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
4575
4520
|
:type usa_state: str
|
|
4576
|
-
:param complete_only:
|
|
4521
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
4577
4522
|
:type complete_only: bool
|
|
4578
|
-
:param include_sequence:
|
|
4523
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
4579
4524
|
:type include_sequence: List[V2ViralSequenceType]
|
|
4580
|
-
:param aux_report:
|
|
4525
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
4581
4526
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
4582
4527
|
:param use_psg: Experimental approach to retrieving sequence data.
|
|
4583
4528
|
:type use_psg: bool
|
|
@@ -4644,19 +4589,19 @@ class VirusApi:
|
|
|
4644
4589
|
@validate_call
|
|
4645
4590
|
def virus_genome_download_accession_without_preload_content(
|
|
4646
4591
|
self,
|
|
4647
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
4592
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
4648
4593
|
taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
|
|
4649
4594
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
4650
4595
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
4651
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
4652
|
-
updated_since: Optional[datetime] = None,
|
|
4653
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
4654
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
4655
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
4656
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
4657
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
4658
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
4659
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
4596
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
4597
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
4598
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
4599
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
4600
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
4601
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
4602
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
4603
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
4604
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
4660
4605
|
use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
|
|
4661
4606
|
filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
|
|
4662
4607
|
_request_timeout: Union[
|
|
@@ -4672,11 +4617,11 @@ class VirusApi:
|
|
|
4672
4617
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
4673
4618
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
4674
4619
|
) -> RESTResponseType:
|
|
4675
|
-
"""
|
|
4620
|
+
"""Get a virus genome data package by nucleotide accession
|
|
4676
4621
|
|
|
4677
|
-
Download a virus genome
|
|
4622
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
|
|
4678
4623
|
|
|
4679
|
-
:param accessions:
|
|
4624
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
4680
4625
|
:type accessions: List[str]
|
|
4681
4626
|
:param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
|
|
4682
4627
|
:type taxons: List[str]
|
|
@@ -4684,23 +4629,23 @@ class VirusApi:
|
|
|
4684
4629
|
:type refseq_only: bool
|
|
4685
4630
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
4686
4631
|
:type annotated_only: bool
|
|
4687
|
-
:param released_since:
|
|
4632
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
4688
4633
|
:type released_since: datetime
|
|
4689
|
-
:param updated_since:
|
|
4634
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
4690
4635
|
:type updated_since: datetime
|
|
4691
|
-
:param host:
|
|
4636
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
4692
4637
|
:type host: str
|
|
4693
|
-
:param pangolin_classification:
|
|
4638
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
4694
4639
|
:type pangolin_classification: str
|
|
4695
|
-
:param geo_location:
|
|
4640
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
4696
4641
|
:type geo_location: str
|
|
4697
|
-
:param usa_state:
|
|
4642
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
4698
4643
|
:type usa_state: str
|
|
4699
|
-
:param complete_only:
|
|
4644
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
4700
4645
|
:type complete_only: bool
|
|
4701
|
-
:param include_sequence:
|
|
4646
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
4702
4647
|
:type include_sequence: List[V2ViralSequenceType]
|
|
4703
|
-
:param aux_report:
|
|
4648
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
4704
4649
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
4705
4650
|
:param use_psg: Experimental approach to retrieving sequence data.
|
|
4706
4651
|
:type use_psg: bool
|
|
@@ -4935,9 +4880,9 @@ class VirusApi:
|
|
|
4935
4880
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
4936
4881
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
4937
4882
|
) -> bytearray:
|
|
4938
|
-
"""Get a virus genome
|
|
4883
|
+
"""Get a virus genome data package
|
|
4939
4884
|
|
|
4940
|
-
|
|
4885
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
|
|
4941
4886
|
|
|
4942
4887
|
:param v2_virus_dataset_request: (required)
|
|
4943
4888
|
:type v2_virus_dataset_request: V2VirusDatasetRequest
|
|
@@ -5006,9 +4951,9 @@ class VirusApi:
|
|
|
5006
4951
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5007
4952
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5008
4953
|
) -> ApiResponse[bytearray]:
|
|
5009
|
-
"""Get a virus genome
|
|
4954
|
+
"""Get a virus genome data package
|
|
5010
4955
|
|
|
5011
|
-
|
|
4956
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
|
|
5012
4957
|
|
|
5013
4958
|
:param v2_virus_dataset_request: (required)
|
|
5014
4959
|
:type v2_virus_dataset_request: V2VirusDatasetRequest
|
|
@@ -5077,9 +5022,9 @@ class VirusApi:
|
|
|
5077
5022
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5078
5023
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5079
5024
|
) -> RESTResponseType:
|
|
5080
|
-
"""Get a virus genome
|
|
5025
|
+
"""Get a virus genome data package
|
|
5081
5026
|
|
|
5082
|
-
|
|
5027
|
+
Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
|
|
5083
5028
|
|
|
5084
5029
|
:param v2_virus_dataset_request: (required)
|
|
5085
5030
|
:type v2_virus_dataset_request: V2VirusDatasetRequest
|
|
@@ -5213,18 +5158,18 @@ class VirusApi:
|
|
|
5213
5158
|
def virus_genome_summary(
|
|
5214
5159
|
self,
|
|
5215
5160
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
5216
|
-
accessions: Annotated[Optional[List[StrictStr]], Field(description="
|
|
5161
|
+
accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
|
|
5217
5162
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
5218
5163
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
5219
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
5220
|
-
updated_since: Optional[datetime] = None,
|
|
5221
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
5222
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
5223
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
5224
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
5225
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
5226
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
5227
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
5164
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
5165
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
5166
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
5167
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
5168
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
5169
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
5170
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
5171
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
5172
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
5228
5173
|
_request_timeout: Union[
|
|
5229
5174
|
None,
|
|
5230
5175
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -5238,35 +5183,35 @@ class VirusApi:
|
|
|
5238
5183
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5239
5184
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5240
5185
|
) -> V2DownloadSummary:
|
|
5241
|
-
"""Get summary
|
|
5186
|
+
"""Get a download summary of a virus genome data package by taxon
|
|
5242
5187
|
|
|
5243
|
-
Get summary
|
|
5188
|
+
Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
|
|
5244
5189
|
|
|
5245
5190
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
5246
5191
|
:type taxon: str
|
|
5247
|
-
:param accessions:
|
|
5192
|
+
:param accessions: One or more nucleotide sequence accessions
|
|
5248
5193
|
:type accessions: List[str]
|
|
5249
5194
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
5250
5195
|
:type refseq_only: bool
|
|
5251
5196
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
5252
5197
|
:type annotated_only: bool
|
|
5253
|
-
:param released_since:
|
|
5198
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
5254
5199
|
:type released_since: datetime
|
|
5255
|
-
:param updated_since:
|
|
5200
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
5256
5201
|
:type updated_since: datetime
|
|
5257
|
-
:param host:
|
|
5202
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
5258
5203
|
:type host: str
|
|
5259
|
-
:param pangolin_classification:
|
|
5204
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
5260
5205
|
:type pangolin_classification: str
|
|
5261
|
-
:param geo_location:
|
|
5206
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
5262
5207
|
:type geo_location: str
|
|
5263
|
-
:param usa_state:
|
|
5208
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
5264
5209
|
:type usa_state: str
|
|
5265
|
-
:param complete_only:
|
|
5210
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
5266
5211
|
:type complete_only: bool
|
|
5267
|
-
:param include_sequence:
|
|
5212
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
5268
5213
|
:type include_sequence: List[V2ViralSequenceType]
|
|
5269
|
-
:param aux_report:
|
|
5214
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
5270
5215
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
5271
5216
|
:param _request_timeout: timeout setting for this request. If one
|
|
5272
5217
|
number provided, it will be total request
|
|
@@ -5328,18 +5273,18 @@ class VirusApi:
|
|
|
5328
5273
|
def virus_genome_summary_with_http_info(
|
|
5329
5274
|
self,
|
|
5330
5275
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
5331
|
-
accessions: Annotated[Optional[List[StrictStr]], Field(description="
|
|
5276
|
+
accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
|
|
5332
5277
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
5333
5278
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
5334
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
5335
|
-
updated_since: Optional[datetime] = None,
|
|
5336
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
5337
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
5338
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
5339
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
5340
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
5341
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
5342
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
5279
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
5280
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
5281
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
5282
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
5283
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
5284
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
5285
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
5286
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
5287
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
5343
5288
|
_request_timeout: Union[
|
|
5344
5289
|
None,
|
|
5345
5290
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -5353,35 +5298,35 @@ class VirusApi:
|
|
|
5353
5298
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5354
5299
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5355
5300
|
) -> ApiResponse[V2DownloadSummary]:
|
|
5356
|
-
"""Get summary
|
|
5301
|
+
"""Get a download summary of a virus genome data package by taxon
|
|
5357
5302
|
|
|
5358
|
-
Get summary
|
|
5303
|
+
Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
|
|
5359
5304
|
|
|
5360
5305
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
5361
5306
|
:type taxon: str
|
|
5362
|
-
:param accessions:
|
|
5307
|
+
:param accessions: One or more nucleotide sequence accessions
|
|
5363
5308
|
:type accessions: List[str]
|
|
5364
5309
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
5365
5310
|
:type refseq_only: bool
|
|
5366
5311
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
5367
5312
|
:type annotated_only: bool
|
|
5368
|
-
:param released_since:
|
|
5313
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
5369
5314
|
:type released_since: datetime
|
|
5370
|
-
:param updated_since:
|
|
5315
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
5371
5316
|
:type updated_since: datetime
|
|
5372
|
-
:param host:
|
|
5317
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
5373
5318
|
:type host: str
|
|
5374
|
-
:param pangolin_classification:
|
|
5319
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
5375
5320
|
:type pangolin_classification: str
|
|
5376
|
-
:param geo_location:
|
|
5321
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
5377
5322
|
:type geo_location: str
|
|
5378
|
-
:param usa_state:
|
|
5323
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
5379
5324
|
:type usa_state: str
|
|
5380
|
-
:param complete_only:
|
|
5325
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
5381
5326
|
:type complete_only: bool
|
|
5382
|
-
:param include_sequence:
|
|
5327
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
5383
5328
|
:type include_sequence: List[V2ViralSequenceType]
|
|
5384
|
-
:param aux_report:
|
|
5329
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
5385
5330
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
5386
5331
|
:param _request_timeout: timeout setting for this request. If one
|
|
5387
5332
|
number provided, it will be total request
|
|
@@ -5443,18 +5388,18 @@ class VirusApi:
|
|
|
5443
5388
|
def virus_genome_summary_without_preload_content(
|
|
5444
5389
|
self,
|
|
5445
5390
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
5446
|
-
accessions: Annotated[Optional[List[StrictStr]], Field(description="
|
|
5391
|
+
accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
|
|
5447
5392
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
5448
5393
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
5449
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
5450
|
-
updated_since: Optional[datetime] = None,
|
|
5451
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
5452
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
5453
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
5454
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
5455
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
5456
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
5457
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
5394
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
5395
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
5396
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
5397
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
5398
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
5399
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
5400
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
5401
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
5402
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
5458
5403
|
_request_timeout: Union[
|
|
5459
5404
|
None,
|
|
5460
5405
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -5468,35 +5413,35 @@ class VirusApi:
|
|
|
5468
5413
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5469
5414
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5470
5415
|
) -> RESTResponseType:
|
|
5471
|
-
"""Get summary
|
|
5416
|
+
"""Get a download summary of a virus genome data package by taxon
|
|
5472
5417
|
|
|
5473
|
-
Get summary
|
|
5418
|
+
Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
|
|
5474
5419
|
|
|
5475
5420
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
5476
5421
|
:type taxon: str
|
|
5477
|
-
:param accessions:
|
|
5422
|
+
:param accessions: One or more nucleotide sequence accessions
|
|
5478
5423
|
:type accessions: List[str]
|
|
5479
5424
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
5480
5425
|
:type refseq_only: bool
|
|
5481
5426
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
5482
5427
|
:type annotated_only: bool
|
|
5483
|
-
:param released_since:
|
|
5428
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
5484
5429
|
:type released_since: datetime
|
|
5485
|
-
:param updated_since:
|
|
5430
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
5486
5431
|
:type updated_since: datetime
|
|
5487
|
-
:param host:
|
|
5432
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
5488
5433
|
:type host: str
|
|
5489
|
-
:param pangolin_classification:
|
|
5434
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
5490
5435
|
:type pangolin_classification: str
|
|
5491
|
-
:param geo_location:
|
|
5436
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
5492
5437
|
:type geo_location: str
|
|
5493
|
-
:param usa_state:
|
|
5438
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
5494
5439
|
:type usa_state: str
|
|
5495
|
-
:param complete_only:
|
|
5440
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
5496
5441
|
:type complete_only: bool
|
|
5497
|
-
:param include_sequence:
|
|
5442
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
5498
5443
|
:type include_sequence: List[V2ViralSequenceType]
|
|
5499
|
-
:param aux_report:
|
|
5444
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
5500
5445
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
5501
5446
|
:param _request_timeout: timeout setting for this request. If one
|
|
5502
5447
|
number provided, it will be total request
|
|
@@ -5713,9 +5658,9 @@ class VirusApi:
|
|
|
5713
5658
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5714
5659
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5715
5660
|
) -> V2DownloadSummary:
|
|
5716
|
-
"""Get summary
|
|
5661
|
+
"""Get a download summary of a virus genome data package
|
|
5717
5662
|
|
|
5718
|
-
Get summary
|
|
5663
|
+
Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
|
|
5719
5664
|
|
|
5720
5665
|
:param v2_virus_dataset_request: (required)
|
|
5721
5666
|
:type v2_virus_dataset_request: V2VirusDatasetRequest
|
|
@@ -5780,9 +5725,9 @@ class VirusApi:
|
|
|
5780
5725
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5781
5726
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5782
5727
|
) -> ApiResponse[V2DownloadSummary]:
|
|
5783
|
-
"""Get summary
|
|
5728
|
+
"""Get a download summary of a virus genome data package
|
|
5784
5729
|
|
|
5785
|
-
Get summary
|
|
5730
|
+
Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
|
|
5786
5731
|
|
|
5787
5732
|
:param v2_virus_dataset_request: (required)
|
|
5788
5733
|
:type v2_virus_dataset_request: V2VirusDatasetRequest
|
|
@@ -5847,9 +5792,9 @@ class VirusApi:
|
|
|
5847
5792
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
5848
5793
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
5849
5794
|
) -> RESTResponseType:
|
|
5850
|
-
"""Get summary
|
|
5795
|
+
"""Get a download summary of a virus genome data package
|
|
5851
5796
|
|
|
5852
|
-
Get summary
|
|
5797
|
+
Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
|
|
5853
5798
|
|
|
5854
5799
|
:param v2_virus_dataset_request: (required)
|
|
5855
5800
|
:type v2_virus_dataset_request: V2VirusDatasetRequest
|
|
@@ -5975,19 +5920,19 @@ class VirusApi:
|
|
|
5975
5920
|
def virus_genome_table(
|
|
5976
5921
|
self,
|
|
5977
5922
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
5978
|
-
accessions: Annotated[Optional[List[StrictStr]], Field(description="
|
|
5923
|
+
accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
|
|
5979
5924
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
5980
5925
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
5981
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
5982
|
-
updated_since: Optional[datetime] = None,
|
|
5983
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
5984
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
5985
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
5986
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
5987
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
5926
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
5927
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
5928
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
5929
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
5930
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
5931
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
5932
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
5988
5933
|
table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
5989
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
5990
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
5934
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
5935
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
5991
5936
|
format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
|
|
5992
5937
|
_request_timeout: Union[
|
|
5993
5938
|
None,
|
|
@@ -6002,37 +5947,37 @@ class VirusApi:
|
|
|
6002
5947
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
6003
5948
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
6004
5949
|
) -> V2TabularOutput:
|
|
6005
|
-
"""
|
|
5950
|
+
"""Get virus genome metadata in a tabular format (deprecated)
|
|
6006
5951
|
|
|
6007
5952
|
Get virus genome metadata in tabular format for virus genomes by taxon.
|
|
6008
5953
|
|
|
6009
5954
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
6010
5955
|
:type taxon: str
|
|
6011
|
-
:param accessions:
|
|
5956
|
+
:param accessions: One or more nucleotide sequence accessions
|
|
6012
5957
|
:type accessions: List[str]
|
|
6013
5958
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
6014
5959
|
:type refseq_only: bool
|
|
6015
5960
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
6016
5961
|
:type annotated_only: bool
|
|
6017
|
-
:param released_since:
|
|
5962
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
6018
5963
|
:type released_since: datetime
|
|
6019
|
-
:param updated_since:
|
|
5964
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
6020
5965
|
:type updated_since: datetime
|
|
6021
|
-
:param host:
|
|
5966
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
6022
5967
|
:type host: str
|
|
6023
|
-
:param pangolin_classification:
|
|
5968
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
6024
5969
|
:type pangolin_classification: str
|
|
6025
|
-
:param geo_location:
|
|
5970
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
6026
5971
|
:type geo_location: str
|
|
6027
|
-
:param usa_state:
|
|
5972
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
6028
5973
|
:type usa_state: str
|
|
6029
|
-
:param complete_only:
|
|
5974
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
6030
5975
|
:type complete_only: bool
|
|
6031
5976
|
:param table_fields: Specify which fields to include in the tabular report
|
|
6032
5977
|
:type table_fields: List[V2VirusTableField]
|
|
6033
|
-
:param include_sequence:
|
|
5978
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
6034
5979
|
:type include_sequence: List[V2ViralSequenceType]
|
|
6035
|
-
:param aux_report:
|
|
5980
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
6036
5981
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
6037
5982
|
:param format: Choose download format (tsv, csv or jsonl)
|
|
6038
5983
|
:type format: V2TableFormat
|
|
@@ -6057,7 +6002,6 @@ class VirusApi:
|
|
|
6057
6002
|
:type _host_index: int, optional
|
|
6058
6003
|
:return: Returns the result object.
|
|
6059
6004
|
""" # noqa: E501
|
|
6060
|
-
warnings.warn("GET /virus/taxon/{taxon}/genome/table is deprecated.", DeprecationWarning)
|
|
6061
6005
|
|
|
6062
6006
|
_param = self._virus_genome_table_serialize(
|
|
6063
6007
|
taxon=taxon,
|
|
@@ -6099,19 +6043,19 @@ class VirusApi:
|
|
|
6099
6043
|
def virus_genome_table_with_http_info(
|
|
6100
6044
|
self,
|
|
6101
6045
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
6102
|
-
accessions: Annotated[Optional[List[StrictStr]], Field(description="
|
|
6046
|
+
accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
|
|
6103
6047
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
6104
6048
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
6105
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
6106
|
-
updated_since: Optional[datetime] = None,
|
|
6107
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
6108
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
6109
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
6110
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
6111
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
6049
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
6050
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
6051
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
6052
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
6053
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
6054
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
6055
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
6112
6056
|
table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
6113
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
6114
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
6057
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
6058
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
6115
6059
|
format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
|
|
6116
6060
|
_request_timeout: Union[
|
|
6117
6061
|
None,
|
|
@@ -6126,37 +6070,37 @@ class VirusApi:
|
|
|
6126
6070
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
6127
6071
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
6128
6072
|
) -> ApiResponse[V2TabularOutput]:
|
|
6129
|
-
"""
|
|
6073
|
+
"""Get virus genome metadata in a tabular format (deprecated)
|
|
6130
6074
|
|
|
6131
6075
|
Get virus genome metadata in tabular format for virus genomes by taxon.
|
|
6132
6076
|
|
|
6133
6077
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
6134
6078
|
:type taxon: str
|
|
6135
|
-
:param accessions:
|
|
6079
|
+
:param accessions: One or more nucleotide sequence accessions
|
|
6136
6080
|
:type accessions: List[str]
|
|
6137
6081
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
6138
6082
|
:type refseq_only: bool
|
|
6139
6083
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
6140
6084
|
:type annotated_only: bool
|
|
6141
|
-
:param released_since:
|
|
6085
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
6142
6086
|
:type released_since: datetime
|
|
6143
|
-
:param updated_since:
|
|
6087
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
6144
6088
|
:type updated_since: datetime
|
|
6145
|
-
:param host:
|
|
6089
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
6146
6090
|
:type host: str
|
|
6147
|
-
:param pangolin_classification:
|
|
6091
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
6148
6092
|
:type pangolin_classification: str
|
|
6149
|
-
:param geo_location:
|
|
6093
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
6150
6094
|
:type geo_location: str
|
|
6151
|
-
:param usa_state:
|
|
6095
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
6152
6096
|
:type usa_state: str
|
|
6153
|
-
:param complete_only:
|
|
6097
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
6154
6098
|
:type complete_only: bool
|
|
6155
6099
|
:param table_fields: Specify which fields to include in the tabular report
|
|
6156
6100
|
:type table_fields: List[V2VirusTableField]
|
|
6157
|
-
:param include_sequence:
|
|
6101
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
6158
6102
|
:type include_sequence: List[V2ViralSequenceType]
|
|
6159
|
-
:param aux_report:
|
|
6103
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
6160
6104
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
6161
6105
|
:param format: Choose download format (tsv, csv or jsonl)
|
|
6162
6106
|
:type format: V2TableFormat
|
|
@@ -6181,7 +6125,6 @@ class VirusApi:
|
|
|
6181
6125
|
:type _host_index: int, optional
|
|
6182
6126
|
:return: Returns the result object.
|
|
6183
6127
|
""" # noqa: E501
|
|
6184
|
-
warnings.warn("GET /virus/taxon/{taxon}/genome/table is deprecated.", DeprecationWarning)
|
|
6185
6128
|
|
|
6186
6129
|
_param = self._virus_genome_table_serialize(
|
|
6187
6130
|
taxon=taxon,
|
|
@@ -6223,19 +6166,19 @@ class VirusApi:
|
|
|
6223
6166
|
def virus_genome_table_without_preload_content(
|
|
6224
6167
|
self,
|
|
6225
6168
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
6226
|
-
accessions: Annotated[Optional[List[StrictStr]], Field(description="
|
|
6169
|
+
accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
|
|
6227
6170
|
refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
6228
6171
|
annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
6229
|
-
released_since: Annotated[Optional[datetime], Field(description="
|
|
6230
|
-
updated_since: Optional[datetime] = None,
|
|
6231
|
-
host: Annotated[Optional[StrictStr], Field(description="
|
|
6232
|
-
pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
6233
|
-
geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
6234
|
-
usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
6235
|
-
complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
6172
|
+
released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
6173
|
+
updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
6174
|
+
host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
6175
|
+
pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
6176
|
+
geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
6177
|
+
usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
6178
|
+
complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
6236
6179
|
table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
6237
|
-
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="
|
|
6238
|
-
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="
|
|
6180
|
+
include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
|
|
6181
|
+
aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
|
|
6239
6182
|
format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
|
|
6240
6183
|
_request_timeout: Union[
|
|
6241
6184
|
None,
|
|
@@ -6250,37 +6193,37 @@ class VirusApi:
|
|
|
6250
6193
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
6251
6194
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
6252
6195
|
) -> RESTResponseType:
|
|
6253
|
-
"""
|
|
6196
|
+
"""Get virus genome metadata in a tabular format (deprecated)
|
|
6254
6197
|
|
|
6255
6198
|
Get virus genome metadata in tabular format for virus genomes by taxon.
|
|
6256
6199
|
|
|
6257
6200
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
6258
6201
|
:type taxon: str
|
|
6259
|
-
:param accessions:
|
|
6202
|
+
:param accessions: One or more nucleotide sequence accessions
|
|
6260
6203
|
:type accessions: List[str]
|
|
6261
6204
|
:param refseq_only: If true, limit results to RefSeq genomes.
|
|
6262
6205
|
:type refseq_only: bool
|
|
6263
6206
|
:param annotated_only: If true, limit results to annotated genomes.
|
|
6264
6207
|
:type annotated_only: bool
|
|
6265
|
-
:param released_since:
|
|
6208
|
+
:param released_since: Limit to genomes released on or after the specified date.
|
|
6266
6209
|
:type released_since: datetime
|
|
6267
|
-
:param updated_since:
|
|
6210
|
+
:param updated_since: Limit to genomes updated on or after the specified date.
|
|
6268
6211
|
:type updated_since: datetime
|
|
6269
|
-
:param host:
|
|
6212
|
+
:param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
6270
6213
|
:type host: str
|
|
6271
|
-
:param pangolin_classification:
|
|
6214
|
+
:param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
6272
6215
|
:type pangolin_classification: str
|
|
6273
|
-
:param geo_location:
|
|
6216
|
+
:param geo_location: Limit to genomes collected from the specified geographic location.
|
|
6274
6217
|
:type geo_location: str
|
|
6275
|
-
:param usa_state:
|
|
6218
|
+
:param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
6276
6219
|
:type usa_state: str
|
|
6277
|
-
:param complete_only:
|
|
6220
|
+
:param complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
6278
6221
|
:type complete_only: bool
|
|
6279
6222
|
:param table_fields: Specify which fields to include in the tabular report
|
|
6280
6223
|
:type table_fields: List[V2VirusTableField]
|
|
6281
|
-
:param include_sequence:
|
|
6224
|
+
:param include_sequence: Specify which sequence files to include in the data package.
|
|
6282
6225
|
:type include_sequence: List[V2ViralSequenceType]
|
|
6283
|
-
:param aux_report:
|
|
6226
|
+
:param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
|
|
6284
6227
|
:type aux_report: List[V2VirusDatasetReportType]
|
|
6285
6228
|
:param format: Choose download format (tsv, csv or jsonl)
|
|
6286
6229
|
:type format: V2TableFormat
|
|
@@ -6305,7 +6248,6 @@ class VirusApi:
|
|
|
6305
6248
|
:type _host_index: int, optional
|
|
6306
6249
|
:return: Returns the result object.
|
|
6307
6250
|
""" # noqa: E501
|
|
6308
|
-
warnings.warn("GET /virus/taxon/{taxon}/genome/table is deprecated.", DeprecationWarning)
|
|
6309
6251
|
|
|
6310
6252
|
_param = self._virus_genome_table_serialize(
|
|
6311
6253
|
taxon=taxon,
|
|
@@ -6499,20 +6441,20 @@ class VirusApi:
|
|
|
6499
6441
|
@validate_call
|
|
6500
6442
|
def virus_reports_by_acessions(
|
|
6501
6443
|
self,
|
|
6502
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
6444
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
6503
6445
|
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
6504
6446
|
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
6505
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
6506
|
-
filter_updated_since: Optional[datetime] = None,
|
|
6507
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
6508
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
6509
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
6510
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
6511
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
6512
|
-
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return
|
|
6447
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
6448
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
6449
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
6450
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
6451
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
6452
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
6453
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
6454
|
+
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
|
|
6513
6455
|
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
6514
6456
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
6515
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
6457
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
6516
6458
|
_request_timeout: Union[
|
|
6517
6459
|
None,
|
|
6518
6460
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -6526,37 +6468,37 @@ class VirusApi:
|
|
|
6526
6468
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
6527
6469
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
6528
6470
|
) -> V2reportsVirusDataReportPage:
|
|
6529
|
-
"""Get virus
|
|
6471
|
+
"""Get a virus data report by nucleotide accession
|
|
6530
6472
|
|
|
6531
|
-
Get virus
|
|
6473
|
+
Get a virus data report by nucleotide accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
6532
6474
|
|
|
6533
|
-
:param accessions:
|
|
6475
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
6534
6476
|
:type accessions: List[str]
|
|
6535
6477
|
:param filter_refseq_only: If true, limit results to RefSeq genomes.
|
|
6536
6478
|
:type filter_refseq_only: bool
|
|
6537
6479
|
:param filter_annotated_only: If true, limit results to annotated genomes.
|
|
6538
6480
|
:type filter_annotated_only: bool
|
|
6539
|
-
:param filter_released_since:
|
|
6481
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
6540
6482
|
:type filter_released_since: datetime
|
|
6541
|
-
:param filter_updated_since:
|
|
6483
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
6542
6484
|
:type filter_updated_since: datetime
|
|
6543
|
-
:param filter_host:
|
|
6485
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
6544
6486
|
:type filter_host: str
|
|
6545
|
-
:param filter_pangolin_classification:
|
|
6487
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
6546
6488
|
:type filter_pangolin_classification: str
|
|
6547
|
-
:param filter_geo_location:
|
|
6489
|
+
:param filter_geo_location: Limit to genomes collected from the specified geographic location.
|
|
6548
6490
|
:type filter_geo_location: str
|
|
6549
|
-
:param filter_usa_state:
|
|
6491
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
6550
6492
|
:type filter_usa_state: str
|
|
6551
|
-
:param filter_complete_only:
|
|
6493
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
6552
6494
|
:type filter_complete_only: bool
|
|
6553
|
-
:param returned_content: Return
|
|
6495
|
+
:param returned_content: Return complete virus reports or nucleotide accessions only
|
|
6554
6496
|
:type returned_content: V2VirusDataReportRequestContentType
|
|
6555
6497
|
:param table_fields: Specify which fields to include in the tabular report
|
|
6556
6498
|
:type table_fields: List[str]
|
|
6557
6499
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
6558
6500
|
:type page_size: int
|
|
6559
|
-
:param page_token: A page token is returned
|
|
6501
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
6560
6502
|
:type page_token: str
|
|
6561
6503
|
:param _request_timeout: timeout setting for this request. If one
|
|
6562
6504
|
number provided, it will be total request
|
|
@@ -6618,20 +6560,20 @@ class VirusApi:
|
|
|
6618
6560
|
@validate_call
|
|
6619
6561
|
def virus_reports_by_acessions_with_http_info(
|
|
6620
6562
|
self,
|
|
6621
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
6563
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
6622
6564
|
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
6623
6565
|
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
6624
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
6625
|
-
filter_updated_since: Optional[datetime] = None,
|
|
6626
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
6627
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
6628
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
6629
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
6630
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
6631
|
-
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return
|
|
6566
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
6567
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
6568
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
6569
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
6570
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
6571
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
6572
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
6573
|
+
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
|
|
6632
6574
|
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
6633
6575
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
6634
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
6576
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
6635
6577
|
_request_timeout: Union[
|
|
6636
6578
|
None,
|
|
6637
6579
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -6645,37 +6587,37 @@ class VirusApi:
|
|
|
6645
6587
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
6646
6588
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
6647
6589
|
) -> ApiResponse[V2reportsVirusDataReportPage]:
|
|
6648
|
-
"""Get virus
|
|
6590
|
+
"""Get a virus data report by nucleotide accession
|
|
6649
6591
|
|
|
6650
|
-
Get virus
|
|
6592
|
+
Get a virus data report by nucleotide accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
6651
6593
|
|
|
6652
|
-
:param accessions:
|
|
6594
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
6653
6595
|
:type accessions: List[str]
|
|
6654
6596
|
:param filter_refseq_only: If true, limit results to RefSeq genomes.
|
|
6655
6597
|
:type filter_refseq_only: bool
|
|
6656
6598
|
:param filter_annotated_only: If true, limit results to annotated genomes.
|
|
6657
6599
|
:type filter_annotated_only: bool
|
|
6658
|
-
:param filter_released_since:
|
|
6600
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
6659
6601
|
:type filter_released_since: datetime
|
|
6660
|
-
:param filter_updated_since:
|
|
6602
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
6661
6603
|
:type filter_updated_since: datetime
|
|
6662
|
-
:param filter_host:
|
|
6604
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
6663
6605
|
:type filter_host: str
|
|
6664
|
-
:param filter_pangolin_classification:
|
|
6606
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
6665
6607
|
:type filter_pangolin_classification: str
|
|
6666
|
-
:param filter_geo_location:
|
|
6608
|
+
:param filter_geo_location: Limit to genomes collected from the specified geographic location.
|
|
6667
6609
|
:type filter_geo_location: str
|
|
6668
|
-
:param filter_usa_state:
|
|
6610
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
6669
6611
|
:type filter_usa_state: str
|
|
6670
|
-
:param filter_complete_only:
|
|
6612
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
6671
6613
|
:type filter_complete_only: bool
|
|
6672
|
-
:param returned_content: Return
|
|
6614
|
+
:param returned_content: Return complete virus reports or nucleotide accessions only
|
|
6673
6615
|
:type returned_content: V2VirusDataReportRequestContentType
|
|
6674
6616
|
:param table_fields: Specify which fields to include in the tabular report
|
|
6675
6617
|
:type table_fields: List[str]
|
|
6676
6618
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
6677
6619
|
:type page_size: int
|
|
6678
|
-
:param page_token: A page token is returned
|
|
6620
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
6679
6621
|
:type page_token: str
|
|
6680
6622
|
:param _request_timeout: timeout setting for this request. If one
|
|
6681
6623
|
number provided, it will be total request
|
|
@@ -6737,20 +6679,20 @@ class VirusApi:
|
|
|
6737
6679
|
@validate_call
|
|
6738
6680
|
def virus_reports_by_acessions_without_preload_content(
|
|
6739
6681
|
self,
|
|
6740
|
-
accessions: Annotated[List[StrictStr], Field(description="
|
|
6682
|
+
accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
|
|
6741
6683
|
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
6742
6684
|
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
6743
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
6744
|
-
filter_updated_since: Optional[datetime] = None,
|
|
6745
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
6746
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
6747
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
6748
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
6749
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
6750
|
-
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return
|
|
6685
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
6686
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
6687
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
6688
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
6689
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
6690
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
6691
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
6692
|
+
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
|
|
6751
6693
|
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
6752
6694
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
6753
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
6695
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
6754
6696
|
_request_timeout: Union[
|
|
6755
6697
|
None,
|
|
6756
6698
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -6764,37 +6706,37 @@ class VirusApi:
|
|
|
6764
6706
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
6765
6707
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
6766
6708
|
) -> RESTResponseType:
|
|
6767
|
-
"""Get virus
|
|
6709
|
+
"""Get a virus data report by nucleotide accession
|
|
6768
6710
|
|
|
6769
|
-
Get virus
|
|
6711
|
+
Get a virus data report by nucleotide accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
6770
6712
|
|
|
6771
|
-
:param accessions:
|
|
6713
|
+
:param accessions: One or more nucleotide sequence accessions (required)
|
|
6772
6714
|
:type accessions: List[str]
|
|
6773
6715
|
:param filter_refseq_only: If true, limit results to RefSeq genomes.
|
|
6774
6716
|
:type filter_refseq_only: bool
|
|
6775
6717
|
:param filter_annotated_only: If true, limit results to annotated genomes.
|
|
6776
6718
|
:type filter_annotated_only: bool
|
|
6777
|
-
:param filter_released_since:
|
|
6719
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
6778
6720
|
:type filter_released_since: datetime
|
|
6779
|
-
:param filter_updated_since:
|
|
6721
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
6780
6722
|
:type filter_updated_since: datetime
|
|
6781
|
-
:param filter_host:
|
|
6723
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
6782
6724
|
:type filter_host: str
|
|
6783
|
-
:param filter_pangolin_classification:
|
|
6725
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
6784
6726
|
:type filter_pangolin_classification: str
|
|
6785
|
-
:param filter_geo_location:
|
|
6727
|
+
:param filter_geo_location: Limit to genomes collected from the specified geographic location.
|
|
6786
6728
|
:type filter_geo_location: str
|
|
6787
|
-
:param filter_usa_state:
|
|
6729
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
6788
6730
|
:type filter_usa_state: str
|
|
6789
|
-
:param filter_complete_only:
|
|
6731
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
6790
6732
|
:type filter_complete_only: bool
|
|
6791
|
-
:param returned_content: Return
|
|
6733
|
+
:param returned_content: Return complete virus reports or nucleotide accessions only
|
|
6792
6734
|
:type returned_content: V2VirusDataReportRequestContentType
|
|
6793
6735
|
:param table_fields: Specify which fields to include in the tabular report
|
|
6794
6736
|
:type table_fields: List[str]
|
|
6795
6737
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
6796
6738
|
:type page_size: int
|
|
6797
|
-
:param page_token: A page token is returned
|
|
6739
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
6798
6740
|
:type page_token: str
|
|
6799
6741
|
:param _request_timeout: timeout setting for this request. If one
|
|
6800
6742
|
number provided, it will be total request
|
|
@@ -7018,9 +6960,9 @@ class VirusApi:
|
|
|
7018
6960
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
7019
6961
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
7020
6962
|
) -> V2reportsVirusDataReportPage:
|
|
7021
|
-
"""Get virus
|
|
6963
|
+
"""Get a virus data report
|
|
7022
6964
|
|
|
7023
|
-
Get virus
|
|
6965
|
+
Get a virus data report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
7024
6966
|
|
|
7025
6967
|
:param v2_virus_data_report_request: (required)
|
|
7026
6968
|
:type v2_virus_data_report_request: V2VirusDataReportRequest
|
|
@@ -7085,9 +7027,9 @@ class VirusApi:
|
|
|
7085
7027
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
7086
7028
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
7087
7029
|
) -> ApiResponse[V2reportsVirusDataReportPage]:
|
|
7088
|
-
"""Get virus
|
|
7030
|
+
"""Get a virus data report
|
|
7089
7031
|
|
|
7090
|
-
Get virus
|
|
7032
|
+
Get a virus data report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
7091
7033
|
|
|
7092
7034
|
:param v2_virus_data_report_request: (required)
|
|
7093
7035
|
:type v2_virus_data_report_request: V2VirusDataReportRequest
|
|
@@ -7152,9 +7094,9 @@ class VirusApi:
|
|
|
7152
7094
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
7153
7095
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
7154
7096
|
) -> RESTResponseType:
|
|
7155
|
-
"""Get virus
|
|
7097
|
+
"""Get a virus data report
|
|
7156
7098
|
|
|
7157
|
-
Get virus
|
|
7099
|
+
Get a virus data report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
7158
7100
|
|
|
7159
7101
|
:param v2_virus_data_report_request: (required)
|
|
7160
7102
|
:type v2_virus_data_report_request: V2VirusDataReportRequest
|
|
@@ -7284,17 +7226,17 @@ class VirusApi:
|
|
|
7284
7226
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
7285
7227
|
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
7286
7228
|
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
7287
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
7288
|
-
filter_updated_since: Optional[datetime] = None,
|
|
7289
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
7290
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
7291
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
7292
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
7293
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
7294
|
-
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return
|
|
7229
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
7230
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
7231
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
7232
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
7233
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
7234
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
7235
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
7236
|
+
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
|
|
7295
7237
|
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
7296
7238
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
7297
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
7239
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
7298
7240
|
_request_timeout: Union[
|
|
7299
7241
|
None,
|
|
7300
7242
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -7308,9 +7250,9 @@ class VirusApi:
|
|
|
7308
7250
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
7309
7251
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
7310
7252
|
) -> V2reportsVirusDataReportPage:
|
|
7311
|
-
"""Get virus
|
|
7253
|
+
"""Get a virus data report by taxon
|
|
7312
7254
|
|
|
7313
|
-
Get virus
|
|
7255
|
+
Get a virus data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
7314
7256
|
|
|
7315
7257
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
7316
7258
|
:type taxon: str
|
|
@@ -7318,27 +7260,27 @@ class VirusApi:
|
|
|
7318
7260
|
:type filter_refseq_only: bool
|
|
7319
7261
|
:param filter_annotated_only: If true, limit results to annotated genomes.
|
|
7320
7262
|
:type filter_annotated_only: bool
|
|
7321
|
-
:param filter_released_since:
|
|
7263
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
7322
7264
|
:type filter_released_since: datetime
|
|
7323
|
-
:param filter_updated_since:
|
|
7265
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
7324
7266
|
:type filter_updated_since: datetime
|
|
7325
|
-
:param filter_host:
|
|
7267
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
7326
7268
|
:type filter_host: str
|
|
7327
|
-
:param filter_pangolin_classification:
|
|
7269
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
7328
7270
|
:type filter_pangolin_classification: str
|
|
7329
|
-
:param filter_geo_location:
|
|
7271
|
+
:param filter_geo_location: Limit to genomes collected from the specified geographic location.
|
|
7330
7272
|
:type filter_geo_location: str
|
|
7331
|
-
:param filter_usa_state:
|
|
7273
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
7332
7274
|
:type filter_usa_state: str
|
|
7333
|
-
:param filter_complete_only:
|
|
7275
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
7334
7276
|
:type filter_complete_only: bool
|
|
7335
|
-
:param returned_content: Return
|
|
7277
|
+
:param returned_content: Return complete virus reports or nucleotide accessions only
|
|
7336
7278
|
:type returned_content: V2VirusDataReportRequestContentType
|
|
7337
7279
|
:param table_fields: Specify which fields to include in the tabular report
|
|
7338
7280
|
:type table_fields: List[str]
|
|
7339
7281
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
7340
7282
|
:type page_size: int
|
|
7341
|
-
:param page_token: A page token is returned
|
|
7283
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
7342
7284
|
:type page_token: str
|
|
7343
7285
|
:param _request_timeout: timeout setting for this request. If one
|
|
7344
7286
|
number provided, it will be total request
|
|
@@ -7403,17 +7345,17 @@ class VirusApi:
|
|
|
7403
7345
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
7404
7346
|
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
7405
7347
|
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
7406
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
7407
|
-
filter_updated_since: Optional[datetime] = None,
|
|
7408
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
7409
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
7410
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
7411
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
7412
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
7413
|
-
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return
|
|
7348
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
7349
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
7350
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
7351
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
7352
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
7353
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
7354
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
7355
|
+
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
|
|
7414
7356
|
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
7415
7357
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
7416
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
7358
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
7417
7359
|
_request_timeout: Union[
|
|
7418
7360
|
None,
|
|
7419
7361
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -7427,9 +7369,9 @@ class VirusApi:
|
|
|
7427
7369
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
7428
7370
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
7429
7371
|
) -> ApiResponse[V2reportsVirusDataReportPage]:
|
|
7430
|
-
"""Get virus
|
|
7372
|
+
"""Get a virus data report by taxon
|
|
7431
7373
|
|
|
7432
|
-
Get virus
|
|
7374
|
+
Get a virus data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
7433
7375
|
|
|
7434
7376
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
7435
7377
|
:type taxon: str
|
|
@@ -7437,27 +7379,27 @@ class VirusApi:
|
|
|
7437
7379
|
:type filter_refseq_only: bool
|
|
7438
7380
|
:param filter_annotated_only: If true, limit results to annotated genomes.
|
|
7439
7381
|
:type filter_annotated_only: bool
|
|
7440
|
-
:param filter_released_since:
|
|
7382
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
7441
7383
|
:type filter_released_since: datetime
|
|
7442
|
-
:param filter_updated_since:
|
|
7384
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
7443
7385
|
:type filter_updated_since: datetime
|
|
7444
|
-
:param filter_host:
|
|
7386
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
7445
7387
|
:type filter_host: str
|
|
7446
|
-
:param filter_pangolin_classification:
|
|
7388
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
7447
7389
|
:type filter_pangolin_classification: str
|
|
7448
|
-
:param filter_geo_location:
|
|
7390
|
+
:param filter_geo_location: Limit to genomes collected from the specified geographic location.
|
|
7449
7391
|
:type filter_geo_location: str
|
|
7450
|
-
:param filter_usa_state:
|
|
7392
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
7451
7393
|
:type filter_usa_state: str
|
|
7452
|
-
:param filter_complete_only:
|
|
7394
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
7453
7395
|
:type filter_complete_only: bool
|
|
7454
|
-
:param returned_content: Return
|
|
7396
|
+
:param returned_content: Return complete virus reports or nucleotide accessions only
|
|
7455
7397
|
:type returned_content: V2VirusDataReportRequestContentType
|
|
7456
7398
|
:param table_fields: Specify which fields to include in the tabular report
|
|
7457
7399
|
:type table_fields: List[str]
|
|
7458
7400
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
7459
7401
|
:type page_size: int
|
|
7460
|
-
:param page_token: A page token is returned
|
|
7402
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
7461
7403
|
:type page_token: str
|
|
7462
7404
|
:param _request_timeout: timeout setting for this request. If one
|
|
7463
7405
|
number provided, it will be total request
|
|
@@ -7522,17 +7464,17 @@ class VirusApi:
|
|
|
7522
7464
|
taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
|
|
7523
7465
|
filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
|
|
7524
7466
|
filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
|
|
7525
|
-
filter_released_since: Annotated[Optional[datetime], Field(description="
|
|
7526
|
-
filter_updated_since: Optional[datetime] = None,
|
|
7527
|
-
filter_host: Annotated[Optional[StrictStr], Field(description="
|
|
7528
|
-
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="
|
|
7529
|
-
filter_geo_location: Annotated[Optional[StrictStr], Field(description="
|
|
7530
|
-
filter_usa_state: Annotated[Optional[StrictStr], Field(description="
|
|
7531
|
-
filter_complete_only: Annotated[Optional[StrictBool], Field(description="
|
|
7532
|
-
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return
|
|
7467
|
+
filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
|
|
7468
|
+
filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
|
|
7469
|
+
filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
|
|
7470
|
+
filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
|
|
7471
|
+
filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
|
|
7472
|
+
filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
|
|
7473
|
+
filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
|
|
7474
|
+
returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
|
|
7533
7475
|
table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
|
|
7534
7476
|
page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
|
|
7535
|
-
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned
|
|
7477
|
+
page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
|
|
7536
7478
|
_request_timeout: Union[
|
|
7537
7479
|
None,
|
|
7538
7480
|
Annotated[StrictFloat, Field(gt=0)],
|
|
@@ -7546,9 +7488,9 @@ class VirusApi:
|
|
|
7546
7488
|
_headers: Optional[Dict[StrictStr, Any]] = None,
|
|
7547
7489
|
_host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
|
|
7548
7490
|
) -> RESTResponseType:
|
|
7549
|
-
"""Get virus
|
|
7491
|
+
"""Get a virus data report by taxon
|
|
7550
7492
|
|
|
7551
|
-
Get virus
|
|
7493
|
+
Get a virus data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
|
|
7552
7494
|
|
|
7553
7495
|
:param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
|
|
7554
7496
|
:type taxon: str
|
|
@@ -7556,27 +7498,27 @@ class VirusApi:
|
|
|
7556
7498
|
:type filter_refseq_only: bool
|
|
7557
7499
|
:param filter_annotated_only: If true, limit results to annotated genomes.
|
|
7558
7500
|
:type filter_annotated_only: bool
|
|
7559
|
-
:param filter_released_since:
|
|
7501
|
+
:param filter_released_since: Limit to genomes released on or after the specified date.
|
|
7560
7502
|
:type filter_released_since: datetime
|
|
7561
|
-
:param filter_updated_since:
|
|
7503
|
+
:param filter_updated_since: Limit to genomes updated on or after the specified date.
|
|
7562
7504
|
:type filter_updated_since: datetime
|
|
7563
|
-
:param filter_host:
|
|
7505
|
+
:param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
|
|
7564
7506
|
:type filter_host: str
|
|
7565
|
-
:param filter_pangolin_classification:
|
|
7507
|
+
:param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
|
|
7566
7508
|
:type filter_pangolin_classification: str
|
|
7567
|
-
:param filter_geo_location:
|
|
7509
|
+
:param filter_geo_location: Limit to genomes collected from the specified geographic location.
|
|
7568
7510
|
:type filter_geo_location: str
|
|
7569
|
-
:param filter_usa_state:
|
|
7511
|
+
:param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
|
|
7570
7512
|
:type filter_usa_state: str
|
|
7571
|
-
:param filter_complete_only:
|
|
7513
|
+
:param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
|
|
7572
7514
|
:type filter_complete_only: bool
|
|
7573
|
-
:param returned_content: Return
|
|
7515
|
+
:param returned_content: Return complete virus reports or nucleotide accessions only
|
|
7574
7516
|
:type returned_content: V2VirusDataReportRequestContentType
|
|
7575
7517
|
:param table_fields: Specify which fields to include in the tabular report
|
|
7576
7518
|
:type table_fields: List[str]
|
|
7577
7519
|
:param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
|
|
7578
7520
|
:type page_size: int
|
|
7579
|
-
:param page_token: A page token is returned
|
|
7521
|
+
:param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
|
|
7580
7522
|
:type page_token: str
|
|
7581
7523
|
:param _request_timeout: timeout setting for this request. If one
|
|
7582
7524
|
number provided, it will be total request
|