变异注释与标识转换：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 Ensembl 变异后果与完整注释¶

dnakit.databases.ensembl_var_get_variant_consequences(*, variant_id, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`variant_id`	string	必填	dbSNP rsID of the variant. Examples: 'rs429358' (APOE), 'rs7903146' (TCF7L2), 'rs1042779'.
`species`	string	None	Species name. Default 'human'. Examples: 'human', 'homo_sapiens'.
`verbose`	bool	True	运行提示开关。

使用 HGVS 表达式进行 VEP 变异注释¶

dnakit.databases.ensembl_vep_annotate_hgvs(*, hgvs_notation, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`hgvs_notation`	string	必填	Variant in HGVS notation. Supports protein (p.), coding DNA (c.), and genomic (g.) notation. Examples: 'BRAF:p.Val600Glu', 'ENST00000366667:c.803C>T', 'NC_000007.14:g.140753336A>T'.
`species`	string	None	Species name. Default: 'human'. Other options: 'mouse', 'rat', 'zebrafish', etc.
`verbose`	bool	True	运行提示开关。

使用 rsID 进行 VEP 变异注释¶

dnakit.databases.ensembl_vep_annotate_rsid(*, variant_id=None, rsid=None, rs_id=None, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`variant_id`	string	None	dbSNP rs identifier. Examples: 'rs7903146' (TCF7L2, type 2 diabetes), 'rs429358' (APOE, Alzheimer's), 'rs1801133' (MTHFR C677T). Aliases: rsid, rs_id.
`rsid`	string	None	Alias for variant_id. dbSNP rs identifier (e.g., 'rs7903146').
`rs_id`	string	None	Alias for variant_id. dbSNP rs identifier (e.g., 'rs7903146').
`species`	string	None	Species name. Default: 'human'.
`verbose`	bool	True	运行提示开关。

按基因组位置进行 VEP 变异注释¶

dnakit.databases.ensembl_vep_region(*, species, region, allele=None, AncestralAllele=None, Blosum62=None, CADD=None, Conservation=None, DisGeNET=None, GeneSplicer=None, GO=None, LoF=None, MaxEntScan=None, Phenotypes=None, SIFT=None, PolyPhen=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`species`	string	必填	Species (e.g., 'human', 'homo_sapiens')
`region`	string	必填	Genomic region with variant (e.g., '21:25891796-25891796')
`allele`	string	None	VEP 区域变异的等位基因参数，遵循 Ensembl VEP 格式。
`AncestralAllele`	integer	None	Include ancestral allele information
`Blosum62`	integer	None	Include BLOSUM62 protein conservation score
`CADD`	integer	None	Include CADD scores
`Conservation`	integer	None	Include conservation scores
`DisGeNET`	integer	None	Include DisGeNET disease associations
`GeneSplicer`	integer	None	Include GeneSplicer predictions
`GO`	integer	None	Include Gene Ontology terms
`LoF`	integer	None	Include Loss-of-Function predictions
`MaxEntScan`	integer	None	Include MaxEntScan splice predictions
`Phenotypes`	integer	None	Include phenotype annotations
`SIFT`	string	None	SIFT prediction: p=prediction, s=score, b=both
`PolyPhen`	string	None	PolyPhen prediction: p=prediction, s=score, b=both
`verbose`	bool	True	运行提示开关。

转换变异编号与 HGVS 表达形式¶

dnakit.databases.ensembl_vep_variant_recoder(*, variant_id, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`variant_id`	string	必填	Variant identifier to recode. Accepts: rsID (e.g., 'rs429358'), HGVS notation (e.g., 'AGT:c.803T>C'), SPDI (e.g., 'NC_000019.10:44908683:T:C').
`species`	string	None	Species name. Default: 'human'.
`verbose`	bool	True	运行提示开关。

获取 GRCh38 变异的综合功能注释¶

dnakit.databases.favor_annotate_variant(*, variant, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`variant`	string	必填	GRCh38 SNV/indel as chr-pos-ref-alt. Accepts '19-44908822-C-T', 'chr19:44908822:C:T', etc.
`verbose`	bool	True	运行提示开关。

按 HGVS 或 rsID 查询综合变异注释¶

dnakit.databases.my_variant_get_variant_annotation(*, variant_id, fields=None, assembly=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`variant_id`	string	必填	HGVS variant ID (e.g., 'chr1:g.2186318G>A') or rsID (e.g., 'rs123'). An HGVS id must be expressed in the assembly given by the 'assembly' parameter.
`fields`	string	None	Fields to return. Useful fields: dbsnp, clinvar, cadd, gnomad_genome, gnomad_exome, dbnsfp (functional predictions).
`assembly`	string	None	Reference genome assembly for both the HGVS variant_id and the returned coordinates: 'hg19' (GRCh37, the default) or 'hg38' (GRCh38).
`verbose`	bool	True	运行提示开关。

按基因、位置或临床意义检索变异¶

dnakit.databases.my_variant_query_variants(*, query=None, fields=None, size=None, assembly=None, variant_id=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`query`	string	None	Search query. Examples: 'rs58991260' (rsID), 'chr7:g.55249071G>A' (HGVS), 'clinvar.gene.symbol:BRCA1' (gene in ClinVar), 'cadd.phred:>30' (high CADD score).
`fields`	string	None	Comma-separated fields to return. Common: dbsnp, clinvar, cadd, gnomad_genome, dbnsfp.
`size`	integer	None	Maximum number of results (1-100).
`assembly`	string	None	Reference genome assembly for the coordinates in the query and in the results: 'hg19' (GRCh37, the default) or 'hg38' (GRCh38).
`variant_id`	string	None	DNAKit optional alias for query
`verbose`	bool	True	运行提示开关。

校验并转换 HGVS 变异描述¶

dnakit.databases.variant_validator_validate_variant(*, genome_build, variant_description, select_transcripts, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`genome_build`	string	必填	Reference genome assembly: 'GRCh37' (hg19) or 'GRCh38' (hg38)
`variant_description`	string	必填	HGVS variant description (e.g., 'NM_007294.4:c.5266dup' for BRCA1 c.5266dupC, 'NM_000179.3:c.943C>T', 'chr17:g.43092919del')
`select_transcripts`	string	必填	Transcript to validate against (e.g., 'NM_007294.4'). Use 'all' to get all transcripts for a genomic variant.
`verbose`	bool	True	运行提示开关。