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变异效应评分与实验数据：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。

查询整条蛋白质的 AlphaMissense 致病性分类

dnakit.databases.alpha_missense_get_protein_scores(*, uniprot_id, max_residues=None, verbose=True)

参数 类型 必填 / 默认值 说明与约束
uniprot_id string 必填 UniProt accession ID (e.g., 'P00533' for EGFR, 'P01116' for KRAS, 'P04637' for TP53).
max_residues integer | null None Optional cap on the number of residues fetched. 0 / null / omitted = no cap (fetch every residue of the protein, recommended for whole-protein analysis). Positive integer = fetch only the first N residues (useful for fast diagnostic calls on very long proteins).
verbose bool True 运行提示开关。

查询蛋白质指定位点的替换分类与平均评分

dnakit.databases.alpha_missense_get_residue_scores(*, uniprot_id, position, verbose=True)

参数 类型 必填 / 默认值 说明与约束
uniprot_id string 必填 UniProt accession ID (e.g., 'P00533' for EGFR)
position integer 必填 Amino acid position in the protein (1-indexed)
verbose bool True 运行提示开关。

查询单个错义变异的 AlphaMissense 分类

dnakit.databases.alpha_missense_get_variant_score(*, uniprot_id, variant, verbose=True)

参数 类型 必填 / 默认值 说明与约束
uniprot_id string 必填 UniProt accession ID (e.g., 'P00533' for EGFR)
variant string 必填 Variant in protein notation: p.X123Y or X123Y where X is reference amino acid, 123 is position, Y is variant (e.g., 'p.R123H', 'V600E')
verbose bool True 运行提示开关。

查询基因组指定位点的全部替换 CADD 分数

dnakit.databases.cadd_get_position_scores(*, chrom, pos, version=None, verbose=True)

参数 类型 必填 / 默认值 说明与约束
chrom string 必填 Chromosome (1-22, X, Y, MT)
pos integer 必填 Genomic position (1-based)
version string None CADD version and genome build
verbose bool True 运行提示开关。

查询基因组区间内的 CADD 分数

dnakit.databases.cadd_get_range_scores(*, chrom, start, end, version=None, verbose=True)

参数 类型 必填 / 默认值 说明与约束
chrom string 必填 Chromosome (1-22, X, Y, MT)
start integer 必填 Start position (1-based, inclusive)
end integer 必填 End position (1-based, inclusive). Max range: 100bp.
version string None CADD version and genome build
verbose bool True 运行提示开关。

通过 MyVariant 查询已收录的 CADD 注释

dnakit.databases.cadd_get_scores(*, variant, assembly='hg38', verbose=True)

参数 类型 必填 / 默认值 说明与约束
variant string 必填 用于 MyVariant CADD 注释检索的变异查询条件。
assembly string 'hg38' 参考基因组版本，例如 hg38。
verbose bool True 运行提示开关。

查询单个变异的 CADD 有害性分数

dnakit.databases.cadd_get_variant_score(*, chrom, pos, ref, alt, version=None, include_annotations=None, verbose=True)

参数 类型 必填 / 默认值 说明与约束
chrom string 必填 Chromosome (1-22, X, Y, MT). Can include 'chr' prefix.
pos integer 必填 Genomic position (1-based)
ref string 必填 Reference allele (e.g., 'A', 'G')
alt string 必填 Alternate allele (e.g., 'T', 'C')
version string None CADD version and genome build
include_annotations boolean None Include full annotation details in response
verbose bool True 运行提示开关。

查询基因的 EVE 评分覆盖情况

dnakit.databases.eve_get_gene_info(*, gene_symbol, verbose=True)

参数 类型 必填 / 默认值 说明与约束
gene_symbol string 必填 Gene symbol (e.g., 'TP53', 'BRCA1', 'EGFR')
verbose bool True 运行提示开关。

查询变异的 EVE 致病性分数

dnakit.databases.eve_get_variant_score(*, variant=None, chrom=None, pos=None, ref=None, alt=None, species=None, verbose=True)

参数 类型 必填 / 默认值 说明与约束
variant string None Variant in HGVS format (e.g., 'ENST00000269305.4:c.100G>A', 'NM_000546.5:c.215C>G')
chrom string None Chromosome (1-22, X, Y). Use with pos, ref, alt instead of variant.
pos integer None Genomic position (GRCh38)
ref string None Reference allele
alt string None Alternate allele
species string None Species (default: human)
verbose bool True 运行提示开关。

将深度突变扫描数据整理为氨基酸效应矩阵

dnakit.databases.mave_db_get_effect_matrix(*, urn, uniprot_id=None, score_field=None, verbose=True)

参数 类型 必填 / 默认值 说明与约束
urn string 必填 MaveDB score set URN (e.g., 'urn:mavedb:00000115-a-7'). Obtain from MaveDB_search_score_sets.
uniprot_id string | null None Optional UniProt accession (e.g., 'P01116' for KRAS). If supplied, the tool fetches the canonical sequence and verifies the MaveDB position numbering against it via a landmark check; sets numbering_offset and surfaces a warning in numbering_check if the positions don't match (silent off-by-N is the #1 silent bug in DMS analysis).
score_field string | null None Optional explicit column name to use as the variant score (e.g., 'score', 'ddG', 'fitness'). If omitted, tries 'score' → 'ddG' → 'fitness' → first numeric non-HGVS field in that order. The actual field used is reported in data.score_field_used.
verbose bool True 运行提示开关。

汇总变异的多来源致病性预测分数

dnakit.databases.my_variant_get_pathogenicity_scores(*, 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 Variant ID: rsID (e.g., rs45478192) or HGVS genomic (e.g., chr16:g.23635348A>C). Both formats work; an HGVS id must be expressed in the assembly given by the 'assembly' parameter.
fields string None Fields to return (pre-configured for pathogenicity scores)
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。