"use strict"; const {Fragment: _Fragment, jsx: _jsx, jsxs: _jsxs} = arguments[0]; const {useMDXComponents: _provideComponents} = arguments[0]; function _createMdxContent(props) { const _components = { a: "a", annotation: "annotation", code: "code", h2: "h2", h3: "h3", li: "li", math: "math", mi: "mi", mo: "mo", mrow: "mrow", p: "p", path: "path", pre: "pre", semantics: "semantics", span: "span", svg: "svg", ul: "ul", ..._provideComponents(), ...props.components }; return _jsxs(_Fragment, { children: [_jsxs(_components.p, { children: ["讲解见", _jsx(_components.a, { href: "/01.PROJECT/02.BI%26GBC/02.GBC/%E5%88%A9%E7%94%A8%E7%BA%BF%E6%80%A7%E6%A8%A1%E5%9E%8B%E4%BC%B0%E8%AE%A1GBC", "data-fs-resolved-file-path": "/01.PROJECT/02.BI&GBC/02.GBC/利用线性模型估计GBC.md", children: "利用线性模型估计GBC" })] }), "\n", _jsxs(_components.h2, { id: "description", children: [_jsx(_components.a, { className: "heading-link", href: "#description", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "Description"] }), "\n", _jsx(_components.p, { children: "We estimated the GBC using the following linear model based on the genotype data:" }), "\n", _jsx(_components.p, { children: _jsxs(_components.span, { className: "katex", children: [_jsx(_components.span, { className: "katex-mathml", children: _jsx(_components.math, { xmlns: "http://www.w3.org/1998/Math/MathML", children: _jsxs(_components.semantics, { children: [_jsxs(_components.mrow, { children: [_jsx(_components.mi, { children: "y" }), _jsx(_components.mo, { children: "=" }), _jsx(_components.mi, { children: "F" }), _jsx(_components.mi, { children: "b" }), _jsx(_components.mo, { children: "+" }), _jsx(_components.mi, { children: "e" })] }), _jsx(_components.annotation, { encoding: "application/x-tex", children: "y=Fb+e" })] }) }) }), _jsxs(_components.span, { className: "katex-html", "aria-hidden": "true", children: [_jsxs(_components.span, { className: "base", children: [_jsx(_components.span, { className: "strut", style: { height: "0.625em", verticalAlign: "-0.1944em" } }), _jsx(_components.span, { className: "mord mathnormal", style: { marginRight: "0.03588em" }, children: "y" }), _jsx(_components.span, { className: "mspace", style: { marginRight: "0.2778em" } }), _jsx(_components.span, { className: "mrel", children: "=" }), _jsx(_components.span, { className: "mspace", style: { marginRight: "0.2778em" } })] }), _jsxs(_components.span, { className: "base", children: [_jsx(_components.span, { className: "strut", style: { height: "0.7778em", verticalAlign: "-0.0833em" } }), _jsx(_components.span, { className: "mord mathnormal", style: { marginRight: "0.13889em" }, children: "F" }), _jsx(_components.span, { className: "mord mathnormal", children: "b" }), _jsx(_components.span, { className: "mspace", style: { marginRight: "0.2222em" } }), _jsx(_components.span, { className: "mbin", children: "+" }), _jsx(_components.span, { className: "mspace", style: { marginRight: "0.2222em" } })] }), _jsxs(_components.span, { className: "base", children: [_jsx(_components.span, { className: "strut", style: { height: "0.4306em" } }), _jsx(_components.span, { className: "mord mathnormal", children: "e" })] })] })] }) }), "\n", _jsx(_components.p, { children: "Where is the genotype vector of all SNPs of the individual to be estimated, and the SNP genotypes are represented by 0 (AA), 1 (AB), and 2 (BB) respectively. is the allele frequency matrix of , where is the number of breeds in the reference population. The regression coefficient ( ) vector is the GBC of each breed to the individual to be estimated. Then, we solved the linear model using ordinary least squares (OLS) regression, where . We normalized the regression coefficients according to a previous study (He et al., 2018). After the adjustment, all negative regression coefficients were replaced by zeroes and minor contributions were filtered out based on a confidence threshold. Finally, the GBC of a breed was estimated from the ratio of that breed’s regression coefficient over the sum of regression coefficients across all breeds." }), "\n", _jsxs(_components.h2, { id: "file-format", children: [_jsx(_components.a, { className: "heading-link", href: "#file-format", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "File format"] }), "\n", _jsx(_components.p, { children: "等位基因频率文件格式：" }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "CHR:POS\tM\tP\n" }), _jsx(_components.span, { className: "code-line", children: "1:208308\t0.181818\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:208309\t0\t0.152174\n" }), _jsx(_components.span, { className: "code-line", children: "1:224028\t0.232143\t0.0416667\n" }), _jsx(_components.span, { className: "code-line", children: "1:224038\t0.259259\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:230229\t0.0555556\t0.479167\n" }), _jsx(_components.span, { className: "code-line", children: "1:234481\t0.240741\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:234612\t0.44\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:238247\t0.240741\t0.0416667\n" }), _jsx(_components.span, { className: "code-line", children: "1:238321\t0.0357143\t0.291667\n" }), _jsx(_components.span, { className: "code-line", children: "1:266494\t0.339286\t0\n" })] }) }), "\n", _jsx(_components.p, { children: "待测个体基因型文件格式：" }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "CHR:POS\tSM01\tSM02\n" }), _jsx(_components.span, { className: "code-line", children: "1:208308\t1\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:208309\t0\t2\n" }), _jsx(_components.span, { className: "code-line", children: "1:224028\t1\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:224038\t2\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:230229\t0\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:234481\t1\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:234612\t0\t0\n" }), _jsx(_components.span, { className: "code-line", children: "1:238247\t0\t1\n" }), _jsx(_components.span, { className: "code-line", children: "1:238321\t2\t1\n" }), _jsx(_components.span, { className: "code-line", children: "1:266494\t2\t0\n" })] }) }), "\n", _jsxs(_components.h2, { id: "code", children: [_jsx(_components.a, { className: "heading-link", href: "#code", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "Code"] }), "\n", _jsx(_components.pre, { className: "language-r", children: _jsxs(_components.code, { className: "language-R code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 读取基因型和等位基因频率数据" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["genotypes ", _jsx(_components.span, { className: "token operator", children: "<-" }), " scan", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"gt\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "# 假设基因型文件是纯文本格式head" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["head", _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 读取等位基因频率文件，带有列名" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs ", _jsx(_components.span, { className: "token operator", children: "<-" }), " as.matrix", _jsx(_components.span, { className: "token punctuation", children: "(" }), "read.table", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"x\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " header", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "FALSE" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: ["head", _jsx(_components.span, { className: "token punctuation", children: "(" }), "allele_freqs", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 检查数据维度" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "if" }), " ", _jsx(_components.span, { className: "token punctuation", children: "(" }), "length", _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token operator", children: "!=" }), " nrow", _jsx(_components.span, { className: "token punctuation", children: "(" }), "allele_freqs", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token punctuation", children: "{" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" stop", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"基因型数据和等位基因频率数据的维度不匹配!\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token punctuation", children: "}" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 构建线性模型，无截距" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# -1 不是指数值，而是告诉R要用无截距模型。用来指定模型中不包含截距项" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 因为多了截距之后，会有多个解" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["model ", _jsx(_components.span, { className: "token operator", children: "<-" }), " lm", _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotypes ", _jsx(_components.span, { className: "token operator", children: "~" }), " allele_freqs ", _jsx(_components.span, { className: "token operator", children: "-" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 查看模型摘要" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["summary", _jsx(_components.span, { className: "token punctuation", children: "(" }), "model", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 提取系数（b向量）" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["coefficients ", _jsx(_components.span, { className: "token operator", children: "<-" }), " coef", _jsx(_components.span, { className: "token punctuation", children: "(" }), "model", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 将负系数转换为0" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["coefficients", _jsx(_components.span, { className: "token punctuation", children: "[" }), "coefficients ", _jsx(_components.span, { className: "token operator", children: "<" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "<-" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 计算每个品种的遗传贡献比例" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["contributions ", _jsx(_components.span, { className: "token operator", children: "<-" }), " coefficients ", _jsx(_components.span, { className: "token operator", children: "/" }), " sum", _jsx(_components.span, { className: "token punctuation", children: "(" }), "coefficients", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 输出结果" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "contributions\n" }), _jsx(_components.span, { className: "code-line", children: "\n" })] }) }), "\n", _jsx(_components.p, { children: "还存在问题：" }), "\n", _jsxs(_components.ul, { children: ["\n", _jsx(_components.li, { children: "这只是一个个体的求解，怎么把多个品种批量做" }), "\n"] }), "\n", _jsx(_components.p, { children: "用python实现了一版，可以多个个体，每行一个：" }), "\n", _jsx(_components.pre, { className: "language-python", children: _jsxs(_components.code, { className: "language-python code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " numpy ", _jsx(_components.span, { className: "token keyword", children: "as" }), " np\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " pandas ", _jsx(_components.span, { className: "token keyword", children: "as" }), " pd\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " statsmodels", _jsx(_components.span, { className: "token punctuation", children: "." }), "api ", _jsx(_components.span, { className: "token keyword", children: "as" }), " sm\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 读取等位基因频率数据" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "read_table", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'x'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " header", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "None" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 强制转换为数值类型，错误转换为NaN" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs ", _jsx(_components.span, { className: "token operator", children: "=" }), " allele_freqs", _jsx(_components.span, { className: "token punctuation", children: "." }), _jsx(_components.span, { className: "token builtin", children: "apply" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "to_numeric", _jsx(_components.span, { className: "token punctuation", children: "," }), " errors", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'coerce'" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "." }), "fillna", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs_matrix ", _jsx(_components.span, { className: "token operator", children: "=" }), " allele_freqs", _jsx(_components.span, { className: "token punctuation", children: "." }), "values\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 读取个体基因型数据" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["genotypes ", _jsx(_components.span, { className: "token operator", children: "=" }), " np", _jsx(_components.span, { className: "token punctuation", children: "." }), "loadtxt", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'gt.trans'" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 确保genotypes始终是二维的" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["genotypes ", _jsx(_components.span, { className: "token operator", children: "=" }), " np", _jsx(_components.span, { className: "token punctuation", children: "." }), "atleast_2d", _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 检查数据维度，确保它们匹配等位基因频率的行数" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "if" }), " genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "!=" }), " allele_freqs_matrix", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "raise" }), " ValueError", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"基因型数据和等位基因频率数据的维度不匹配!\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 初始化存储每个个体GBC的结果" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["individual_contributions ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "DataFrame", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 循环处理每个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "for" }), " i ", _jsx(_components.span, { className: "token keyword", children: "in" }), " ", _jsx(_components.span, { className: "token builtin", children: "range" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " ", _jsx(_components.span, { className: "token comment", children: "# 注意这里改为genotypes.shape[0]，因为每行是一个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" genotype ", _jsx(_components.span, { className: "token operator", children: "=" }), " genotypes", _jsx(_components.span, { className: "token punctuation", children: "[" }), "i", _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token punctuation", children: ":" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token comment", children: "# 获取第i个个体的基因型数据" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 构建线性模型，无截距" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" y ", _jsx(_components.span, { className: "token operator", children: "=" }), " genotype\n"] }), _jsxs(_components.span, { className: "code-line", children: [" X ", _jsx(_components.span, { className: "token operator", children: "=" }), " allele_freqs_matrix\n"] }), _jsxs(_components.span, { className: "code-line", children: [" model ", _jsx(_components.span, { className: "token operator", children: "=" }), " sm", _jsx(_components.span, { className: "token punctuation", children: "." }), "OLS", _jsx(_components.span, { className: "token punctuation", children: "(" }), "y", _jsx(_components.span, { className: "token punctuation", children: "," }), " X", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" results ", _jsx(_components.span, { className: "token operator", children: "=" }), " model", _jsx(_components.span, { className: "token punctuation", children: "." }), "fit", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 提取系数（b向量）" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" coefficients ", _jsx(_components.span, { className: "token operator", children: "=" }), " results", _jsx(_components.span, { className: "token punctuation", children: "." }), "params\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 将负系数转换为0" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" coefficients", _jsx(_components.span, { className: "token punctuation", children: "[" }), "coefficients ", _jsx(_components.span, { className: "token operator", children: "<" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 计算每个品种的遗传贡献比例" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions ", _jsx(_components.span, { className: "token operator", children: "=" }), " coefficients ", _jsx(_components.span, { className: "token operator", children: "/" }), " ", _jsx(_components.span, { className: "token builtin", children: "sum" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "coefficients", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 将结果添加到DataFrame中" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" individual_contributions", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsxs(_components.span, { className: "token string-interpolation", children: [_jsx(_components.span, { className: "token string", children: "f'Individual_" }), _jsxs(_components.span, { className: "token interpolation", children: [_jsx(_components.span, { className: "token punctuation", children: "{" }), "i", _jsx(_components.span, { className: "token operator", children: "+" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "}" })] }), _jsx(_components.span, { className: "token string", children: "'" })] }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " contributions\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 输出结果" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "print" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "individual_contributions", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] })] }) }), "\n", _jsxs(_components.h3, { id: "final-version", children: [_jsx(_components.a, { className: "heading-link", href: "#final-version", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "final version"] }), "\n", _jsx(_components.p, { children: "优化df写入性能，改成每列一个个体：" }), "\n", _jsx(_components.pre, { className: "language-python", children: _jsxs(_components.code, { className: "language-python code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#加上了参考品种名字和待测样本名字" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# gt一列一个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " numpy ", _jsx(_components.span, { className: "token keyword", children: "as" }), " np\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " pandas ", _jsx(_components.span, { className: "token keyword", children: "as" }), " pd\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " statsmodels", _jsx(_components.span, { className: "token punctuation", children: "." }), "api ", _jsx(_components.span, { className: "token keyword", children: "as" }), " sm\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 读取等位基因频率数据，假设第一行是品种名称" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "read_table", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'RAD.merge_MP.frq.fmt'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'\\s+'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " header", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " index_col", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'CHR:POS'" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "# 使用header=0读取列名" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs_matrix ", _jsx(_components.span, { className: "token operator", children: "=" }), " allele_freqs", _jsx(_components.span, { className: "token punctuation", children: "." }), "values\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#读取基因型文件" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["genotypes ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "read_table", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'FinalSNP.filteredmaf01.rename_chr.ex_dup.phased.keepUN.raw.trans.fmt'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'\\s+'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " header", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "set_index", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'CHR:POS'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " inplace", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "True" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 初始化字典来存储每个个体的贡献" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["contributions_dict ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token punctuation", children: "{" }), _jsx(_components.span, { className: "token punctuation", children: "}" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 循环处理每个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "for" }), " i ", _jsx(_components.span, { className: "token keyword", children: "in" }), " ", _jsx(_components.span, { className: "token builtin", children: "range" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " ", _jsx(_components.span, { className: "token comment", children: "# 修改为genotypes.shape[1]，因为每列是一个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" genotype ", _jsx(_components.span, { className: "token operator", children: "=" }), " genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "iloc", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " i", _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "." }), "values ", _jsx(_components.span, { className: "token comment", children: "# 获取第i个个体的基因型数据" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 检查数据维度" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "if" }), " ", _jsx(_components.span, { className: "token builtin", children: "len" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotype", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token operator", children: "!=" }), " allele_freqs_matrix", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "raise" }), " ValueError", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"Dimensions of genotype data and allele frequency data do not match!\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 构建线性模型，无截距" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" X ", _jsx(_components.span, { className: "token operator", children: "=" }), " allele_freqs_matrix\n"] }), _jsxs(_components.span, { className: "code-line", children: [" model ", _jsx(_components.span, { className: "token operator", children: "=" }), " sm", _jsx(_components.span, { className: "token punctuation", children: "." }), "OLS", _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotype", _jsx(_components.span, { className: "token punctuation", children: "," }), " X", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" results ", _jsx(_components.span, { className: "token operator", children: "=" }), " model", _jsx(_components.span, { className: "token punctuation", children: "." }), "fit", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 提取系数（b向量）" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" coefficients ", _jsx(_components.span, { className: "token operator", children: "=" }), " results", _jsx(_components.span, { className: "token punctuation", children: "." }), "params\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 将负系数转换为0" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" coefficients", _jsx(_components.span, { className: "token punctuation", children: "[" }), "coefficients ", _jsx(_components.span, { className: "token operator", children: "<" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 计算每个品种的遗传贡献比例" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions ", _jsx(_components.span, { className: "token operator", children: "=" }), " coefficients ", _jsx(_components.span, { className: "token operator", children: "/" }), " ", _jsx(_components.span, { className: "token builtin", children: "sum" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "coefficients", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 将contributions中小于0.01的系数转换为0" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions", _jsx(_components.span, { className: "token punctuation", children: "[" }), "contributions ", _jsx(_components.span, { className: "token operator", children: "<" }), " ", _jsx(_components.span, { className: "token number", children: "0.02" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 再次计算每个品种的遗传贡献比例" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions ", _jsx(_components.span, { className: "token operator", children: "=" }), " contributions ", _jsx(_components.span, { className: "token operator", children: "/" }), " ", _jsx(_components.span, { className: "token builtin", children: "sum" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "contributions", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 存储到字典" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions_dict", _jsx(_components.span, { className: "token punctuation", children: "[" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "columns", _jsx(_components.span, { className: "token punctuation", children: "[" }), "i", _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " contributions\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 使用字典创建DataFrame，索引设置为品种名称" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["individual_contributions_rounded ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "DataFrame", _jsx(_components.span, { className: "token punctuation", children: "(" }), "contributions_dict", _jsx(_components.span, { className: "token punctuation", children: "," }), " index", _jsx(_components.span, { className: "token operator", children: "=" }), "allele_freqs", _jsx(_components.span, { className: "token punctuation", children: "." }), "columns", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "." }), _jsx(_components.span, { className: "token builtin", children: "round" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token number", children: "4" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#print(individual_contributions_rounded)" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 将结果保存到CSV文件，已经四舍五入" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["individual_contributions_rounded", _jsx(_components.span, { className: "token punctuation", children: "." }), "to_csv", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'GBC.csv'" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] })] }) }), "\n", _jsxs(_components.h3, { id: "非负最小二乘-nnls求解", children: [_jsx(_components.a, { className: "heading-link", href: "#非负最小二乘-nnls求解", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "非负最小二乘 (NNLS)求解"] }), "\n", _jsx(_components.pre, { className: "language-python", children: _jsxs(_components.code, { className: "language-python code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 加上了参考品种名字和待测样本名字" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# gt一列一个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " numpy ", _jsx(_components.span, { className: "token keyword", children: "as" }), " np\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "import" }), " pandas ", _jsx(_components.span, { className: "token keyword", children: "as" }), " pd\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "from" }), " scipy", _jsx(_components.span, { className: "token punctuation", children: "." }), "optimize ", _jsx(_components.span, { className: "token keyword", children: "import" }), " nnls ", _jsx(_components.span, { className: "token comment", children: "# 导入NNLS求解器" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 读取等位基因频率数据，假设第一行是品种名称" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "read_table", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'RAD.merge_MP.frq.fmt'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'\\s+'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " header", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " index_col", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'CHR:POS'" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "# 使用header=0读取列名" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["allele_freqs_matrix ", _jsx(_components.span, { className: "token operator", children: "=" }), " allele_freqs", _jsx(_components.span, { className: "token punctuation", children: "." }), "values\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 读取基因型文件" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["genotypes ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "read_table", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'FinalSNP.filteredmaf01.rename_chr.ex_dup.phased.keepUN.raw.trans.fmt'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'\\s+'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " header", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "set_index", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'CHR:POS'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " inplace", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "True" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 初始化字典来存储每个个体的贡献" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["contributions_dict ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token punctuation", children: "{" }), _jsx(_components.span, { className: "token punctuation", children: "}" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 循环处理每个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "for" }), " i ", _jsx(_components.span, { className: "token keyword", children: "in" }), " ", _jsx(_components.span, { className: "token builtin", children: "range" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " ", _jsx(_components.span, { className: "token comment", children: "# 修改为genotypes.shape[1]，因为每列是一个个体" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" genotype ", _jsx(_components.span, { className: "token operator", children: "=" }), " genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "iloc", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " i", _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "." }), "values ", _jsx(_components.span, { className: "token comment", children: "# 获取第i个个体的基因型数据" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 检查数据维度" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "if" }), " ", _jsx(_components.span, { className: "token builtin", children: "len" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "genotype", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token operator", children: "!=" }), " allele_freqs_matrix", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "raise" }), " ValueError", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "\"Dimensions of genotype data and allele frequency data do not match!\"" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "try" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 使用非负最小二乘 (NNLS) 求解" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" coefficients", _jsx(_components.span, { className: "token punctuation", children: "," }), " _ ", _jsx(_components.span, { className: "token operator", children: "=" }), " nnls", _jsx(_components.span, { className: "token punctuation", children: "(" }), "allele_freqs_matrix", _jsx(_components.span, { className: "token punctuation", children: "," }), " genotype", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 归一化处理" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" total ", _jsx(_components.span, { className: "token operator", children: "=" }), " coefficients", _jsx(_components.span, { className: "token punctuation", children: "." }), _jsx(_components.span, { className: "token builtin", children: "sum" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions ", _jsx(_components.span, { className: "token operator", children: "=" }), " coefficients ", _jsx(_components.span, { className: "token operator", children: "/" }), " total\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 动态阈值（基于数据标准差）" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["\t\tthreshold ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0.5" }), " ", _jsx(_components.span, { className: "token operator", children: "*" }), " np", _jsx(_components.span, { className: "token punctuation", children: "." }), "std", _jsx(_components.span, { className: "token punctuation", children: "(" }), "contributions", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["\t\tcontributions", _jsx(_components.span, { className: "token punctuation", children: "[" }), "contributions ", _jsx(_components.span, { className: "token operator", children: "<" }), " threshold", _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 重新归一化（如果总和不为零）" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" filtered_sum ", _jsx(_components.span, { className: "token operator", children: "=" }), " contributions", _jsx(_components.span, { className: "token punctuation", children: "." }), _jsx(_components.span, { className: "token builtin", children: "sum" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions ", _jsx(_components.span, { className: "token operator", children: "/=" }), " filtered_sum\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 存储到字典" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions_dict", _jsx(_components.span, { className: "token punctuation", children: "[" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "columns", _jsx(_components.span, { className: "token punctuation", children: "[" }), "i", _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " contributions\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "except" }), " Exception ", _jsx(_components.span, { className: "token keyword", children: "as" }), " e", _jsx(_components.span, { className: "token punctuation", children: ":" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "print" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsxs(_components.span, { className: "token string-interpolation", children: [_jsx(_components.span, { className: "token string", children: "f\"Error processing individual " }), _jsxs(_components.span, { className: "token interpolation", children: [_jsx(_components.span, { className: "token punctuation", children: "{" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "columns", _jsx(_components.span, { className: "token punctuation", children: "[" }), "i", _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "}" })] }), _jsx(_components.span, { className: "token string", children: ": " }), _jsxs(_components.span, { className: "token interpolation", children: [_jsx(_components.span, { className: "token punctuation", children: "{" }), _jsx(_components.span, { className: "token builtin", children: "str" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "e", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "}" })] }), _jsx(_components.span, { className: "token string", children: "\"" })] }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token comment", children: "# 存储NaN值作为错误标记" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" contributions_dict", _jsx(_components.span, { className: "token punctuation", children: "[" }), "genotypes", _jsx(_components.span, { className: "token punctuation", children: "." }), "columns", _jsx(_components.span, { className: "token punctuation", children: "[" }), "i", _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " np", _jsx(_components.span, { className: "token punctuation", children: "." }), "full", _jsx(_components.span, { className: "token punctuation", children: "(" }), "allele_freqs_matrix", _jsx(_components.span, { className: "token punctuation", children: "." }), "shape", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " np", _jsx(_components.span, { className: "token punctuation", children: "." }), "nan", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 使用字典创建DataFrame，索引设置为品种名称" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["individual_contributions_rounded ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "DataFrame", _jsx(_components.span, { className: "token punctuation", children: "(" }), "contributions_dict", _jsx(_components.span, { className: "token punctuation", children: "," }), " index", _jsx(_components.span, { className: "token operator", children: "=" }), "allele_freqs", _jsx(_components.span, { className: "token punctuation", children: "." }), "columns", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "." }), _jsx(_components.span, { className: "token builtin", children: "round" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token number", children: "4" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 将结果保存到CSV文件，已经四舍五入" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["individual_contributions_rounded", _jsx(_components.span, { className: "token punctuation", children: "." }), "to_csv", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'GBC_NNLS.csv'" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" })] }) })] }); } function MDXContent(props = {}) { const {wrapper: MDXLayout} = { ..._provideComponents(), ...props.components }; return MDXLayout ? _jsx(MDXLayout, { ...props, children: _jsx(_createMdxContent, { ...props }) }) : _createMdxContent(props); } return { default: MDXContent };