GWAS 研究与关联查询：参数与补充说明¶

用法和示例见功能教程。

各功能按作用、API、输入、输出、示例代码和结果说明介绍。运行前按说明准备凭据、本地文件与可选依赖；远程结果随数据库版本与查询时间变化。

查询指定 SNP 的 GWAS 关联¶

dnakit.databases.gwas_get_associations_for_snp(*, rs_id, sort=None, direction=None, size=None, page=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`rs_id`	string	必填	dbSNP rs identifier
`sort`	string	None	Sort field (e.g., 'p_value', 'or_value')
`direction`	string	None	Sort direction ('asc' or 'desc')
`size`	integer	None	Number of results to return per page
`page`	integer	None	Page number for pagination
`verbose`	bool	True	运行提示开关。

查询指定 GWAS 研究的关联结果¶

dnakit.databases.gwas_get_associations_for_study(*, accession_id, size=None, page=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`accession_id`	string	必填	Study accession identifier
`size`	integer	None	Number of results to return per page
`page`	integer	None	Page number for pagination
`verbose`	bool	True	运行提示开关。

查询指定性状的 GWAS 关联结果¶

dnakit.databases.gwas_get_associations_for_trait(*, disease_trait=None, efo_uri=None, efo_id=None, efo_trait=None, size=None, page=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`disease_trait`	string	None	Disease or trait name for text-based search (e.g., 'diabetes', 'hypertension')
`efo_uri`	string	None	Full EFO ontology URI (e.g., 'http://www.ebi.ac.uk/efo/EFO_0001645')
`efo_id`	string	None	EFO/OBA term ID (e.g., 'EFO_0001645', 'OBA_2050062'). Recommended for reliable trait filtering.
`efo_trait`	string	None	Exact EFO trait label. Use when you know the canonical trait string.
`size`	integer	None	Number of results to return per page
`page`	integer	None	Page number for pagination
`verbose`	bool	True	运行提示开关。

以下参数组必须且只能提供一组：disease_trait; efo_uri; efo_id; efo_trait。

按 rsID 查询 GWAS SNP 详情¶

dnakit.databases.gwas_get_snp_by_id(*, rs_id, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`rs_id`	string	必填	dbSNP rs identifier
`verbose`	bool	True	运行提示开关。

查询映射到指定基因的 GWAS SNP¶

dnakit.databases.gwas_get_snps_for_gene(*, size=None, page=None, gene_symbol=None, gene=None, mapped_gene=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`size`	integer	None	Number of results to return per page
`page`	integer	None	Page number for pagination
`gene_symbol`	string	None	Gene name or symbol (e.g., 'BRCA1', 'TP53', 'GBA')
`gene`	string	None	Alias for gene_symbol
`mapped_gene`	string	None	Alias for gene_symbol
`verbose`	bool	True	运行提示开关。

查询指定性状的 GWAS 研究¶

dnakit.databases.gwas_get_studies_for_trait(*, disease_trait=None, efo_uri=None, efo_id=None, efo_trait=None, cohort=None, gxe=None, full_pvalue_set=None, size=None, page=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`disease_trait`	string	None	Disease or trait name for text-based search (e.g., 'diabetes', 'alzheimer disease')
`efo_uri`	string	None	Full EFO ontology URI (e.g., 'http://www.ebi.ac.uk/efo/EFO_0001645')
`efo_id`	string	None	EFO/OBA term ID (e.g., 'EFO_0001645', 'OBA_2050062'). Recommended for reliable trait filtering.
`efo_trait`	string	None	Exact EFO trait label. Use when you know the canonical trait string.
`cohort`	string	None	Cohort name (e.g., 'UKB' for UK Biobank)
`gxe`	boolean	None	Filter for Gene-by-Environment interaction studies
`full_pvalue_set`	boolean	None	Filter for studies with full summary statistics
`size`	integer	None	Number of results to return per page
`page`	integer	None	Page number for pagination
`verbose`	bool	True	运行提示开关。

以下参数组必须且只能提供一组：disease_trait; efo_uri; efo_id; efo_trait。

按研究编号查询 GWAS 详情¶

dnakit.databases.gwas_get_study_by_id(*, study_id=None, accession_id=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`study_id`	string	None	GWAS study identifier (GCST accession, e.g. 'GCST000392')
`accession_id`	string	None	Alias for study_id -- the same GCST accession identifier, accepted so results from other gwas_* tools (which use the field name 'accession_id') can be passed straight in.
`verbose`	bool	True	运行提示开关。

检索疾病或性状相关的 GWAS 变异¶

dnakit.databases.gwas_get_variants_for_trait(*, disease_trait=None, trait=None, efo_uri=None, efo_id=None, efo_trait=None, size=None, limit=None, page=None, sort=None, direction=None, p_value_threshold=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`disease_trait`	string	None	Disease or trait name for text-based search (e.g., 'diabetes', 'breast cancer')
`trait`	string	None	Alias for disease_trait. Disease or trait name (e.g., 'type 2 diabetes', 'breast cancer')
`efo_uri`	string	None	Full EFO ontology URI (e.g., 'http://www.ebi.ac.uk/efo/EFO_0001645')
`efo_id`	string	None	EFO/OBA term ID (e.g., 'EFO_0001645', 'OBA_2050062'). Recommended for reliable trait filtering.
`efo_trait`	string	None	Exact EFO trait label. Use when you know the canonical trait string.
`size`	integer	None	Number of results to return per page
`limit`	integer	None	Alias for size. Number of results to return per page
`page`	integer	None	Page number for pagination
`sort`	string	None	Sort field (e.g., 'p_value', 'or_value'). Defaults to 'p_value' so the most significant associations appear first.
`direction`	string	None	Sort direction ('asc' or 'desc'). Defaults to 'asc'.
`p_value_threshold`	number	None	对当前返回页应用的 P 值过滤阈值；不代表已遍历全库。
`verbose`	bool	True	运行提示开关。

以下参数组必须且只能提供一组：disease_trait; trait; efo_uri; efo_id; efo_trait。

按关键词检索 GWAS 关联¶

dnakit.databases.gwas_search_associations(*, disease_trait=None, query=None, efo_uri=None, efo_id=None, efo_trait=None, rs_id=None, accession_id=None, p_value=None, p_value_threshold=None, sort=None, direction=None, size=None, page=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`disease_trait`	string	None	Disease or trait name for text-based search (e.g., 'diabetes', 'coronary artery disease', 'breast cancer'). NOTE: GWAS associations are indexed by trait/disease, not by gene or drug name — passing a gene symbol or drug name here will fail. Use efo_id for precise filtering.
`query`	string	None	Alias for disease_trait. Disease or trait name (e.g., 'type 2 diabetes'). NOTE: gene symbols and drug names are not valid GWAS trait queries.
`efo_uri`	string	None	Full EFO ontology URI (e.g., 'http://www.ebi.ac.uk/efo/EFO_0001645')
`efo_id`	string	None	EFO/OBA term ID (e.g., 'EFO_0001645', 'OBA_2050062'). Recommended for reliable trait filtering.
`efo_trait`	string	None	Exact EFO trait label (e.g., 'serum alanine aminotransferase amount'). Use when you know the canonical trait string.
`rs_id`	string	None	dbSNP rs identifier
`accession_id`	string	None	Study accession identifier
`p_value`	number	None	Maximum p-value threshold for filtering (e.g., 5e-8 for genome-wide significance). IMPORTANT: the GWAS Catalog REST API v2 has NO server-side p-value filter (its OpenAPI document lists only pubmed_id, rs_id, full_pvalue_set, accession_id, efo_trait, efo_id, show_child_trait, mapped_gene, extended_geneset, sort, direction, page and size on GET /v2/associations), so this threshold is applied CLIENT-SIDE to the page of associations fetched. To make it meaningful the page is fetched p_value-ascending (most-significant-first) whenever sort is 'p_value' (the default), and the surviving rows are then re-ordered into the direction you asked for. metadata.p_value_filter_scope, metadata.filtered_total and metadata.p_value_filter_note report exactly what was filtered.
`p_value_threshold`	number	None	Alias for p_value: maximum p-value threshold (also applied client-side; see p_value).
`sort`	string	None	Sort field (e.g., 'p_value', 'or_value'). Defaults to 'p_value'. When a p_value threshold is supplied and sort is 'p_value', the upstream page is always fetched ascending so the threshold sees the significant end; metadata.sort_override records this and the returned rows are ordered per your 'direction'.
`direction`	string	None	Sort direction ('asc' or 'desc'). Defaults to 'asc'. Combined with a p_value threshold this orders the RETURNED rows; see metadata.sort_override.
`size`	integer	None	Number of results to return
`page`	integer	None	Page number for pagination
`verbose`	bool	True	运行提示开关。

按基因检索 GWAS 风险等位基因与显著性¶

dnakit.databases.gwas_search_associations_by_gene(*, gene_name, size=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`gene_name`	string	必填	Gene symbol (e.g., BRCA1).
`size`	integer	None	Max associations to return (default 100; results are sorted by p-value, most significant first).
`verbose`	bool	True	运行提示开关。

按 rsID 或基因检索 GWAS SNP¶

dnakit.databases.gwas_search_snps(*, rs_id=None, mapped_gene=None, size=None, page=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`rs_id`	string	None	dbSNP rs identifier
`mapped_gene`	string	None	Gene name or symbol
`size`	integer	None	Number of results to return
`page`	integer	None	Page number for pagination
`verbose`	bool	True	运行提示开关。

按性状与队列条件检索 GWAS 研究¶

dnakit.databases.gwas_search_studies(*, disease_trait=None, efo_uri=None, efo_id=None, efo_trait=None, cohort=None, gxe=None, full_pvalue_set=None, size=None, page=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`disease_trait`	string	None	Disease or trait name for text-based search (e.g., 'diabetes', 'breast cancer')
`efo_uri`	string	None	Full EFO ontology URI (e.g., 'http://www.ebi.ac.uk/efo/EFO_0001645')
`efo_id`	string	None	EFO/OBA term ID (e.g., 'EFO_0001645', 'OBA_2050062'). Recommended for reliable trait filtering.
`efo_trait`	string	None	Exact EFO trait label. Use when you know the canonical trait string.
`cohort`	string	None	Cohort name (e.g., 'UKB' for UK Biobank)
`gxe`	boolean	None	Filter for Gene-by-Environment interaction studies
`full_pvalue_set`	boolean	None	Filter for studies with full summary statistics
`size`	integer	None	Number of results to return
`page`	integer	None	Page number for pagination
`verbose`	bool	True	运行提示开关。