"use strict"; const {Fragment: _Fragment, jsx: _jsx, jsxs: _jsxs} = arguments[0]; const {useMDXComponents: _provideComponents} = arguments[0]; function _createMdxContent(props) { const _components = { a: "a", code: "code", h2: "h2", h3: "h3", li: "li", ol: "ol", p: "p", path: "path", pre: "pre", span: "span", svg: "svg", ..._provideComponents(), ...props.components }; return _jsxs(_Fragment, { children: [_jsxs(_components.h2, { id: "原理", children: [_jsx(_components.a, { className: "heading-link", href: "#原理", 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" }) }) }), "原理"] }), "\n", _jsxs(_components.h2, { id: "具体操作", children: [_jsx(_components.a, { className: "heading-link", href: "#具体操作", 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" }) }) }), "具体操作"] }), "\n", _jsxs(_components.h2, { id: "计算xp-ehh", children: [_jsx(_components.a, { className: "heading-link", href: "#计算xp-ehh", 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" }) }) }), "计算XP-EHH"] }), "\n", _jsx(_components.p, { children: "包括以下步骤：" }), "\n", _jsxs(_components.ol, { children: ["\n", _jsx(_components.li, { children: "分染色体提取map文件，并换算遗传距离" }), "\n", _jsx(_components.li, { children: "分染色体提取两个群体的vcf" }), "\n", _jsx(_components.li, { children: "分染色体计算xpehh，支持多线程" }), "\n", _jsx(_components.li, { children: "根据全局的value进行矫正，所以要一次性把所有的染色体都给到" }), "\n"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 分染色体提取map文件，并重命名snp name，换算遗传距离" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token function", children: "grep" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "-w" }), " ", _jsx(_components.span, { className: "token string", children: "'^1'" }), " /home/guoyingwei/project/LeiQiong_cattle2/00.data/from_raw_vcf/leiqiong.filtered.snp.maf.map ", _jsx(_components.span, { className: "token operator", children: "|" }), _jsx(_components.span, { className: "token function", children: "awk" }), " ", _jsx(_components.span, { className: "token string", children: "'{$3=$4/1000000;print $0}'" }), " ", _jsx(_components.span, { className: "token operator", children: "|" }), _jsx(_components.span, { className: "token function", children: "sed" }), " ", _jsx(_components.span, { className: "token string", children: "'s/ /\\t/g'" }), " ", _jsx(_components.span, { className: "token operator", children: ">" }), " /home/guoyingwei/project/LeiQiong_cattle2/03.selection/05.xpehh/leiqiong.filtered.snp.maf.chr1.map\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 分染色体分别提取两个群体的样本" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "for" }), " ", _jsx(_components.span, { className: "token for-or-select variable", children: "i" }), " ", _jsx(_components.span, { className: "token keyword", children: "in" }), " ", _jsx(_components.span, { className: "token punctuation", children: "{" }), _jsx(_components.span, { className: "token number", children: "2" }), _jsx(_components.span, { className: "token punctuation", children: ".." }), _jsx(_components.span, { className: "token number", children: "29" }), _jsx(_components.span, { className: "token punctuation", children: "}" }), _jsx(_components.span, { className: "token punctuation", children: ";" }), _jsx(_components.span, { className: "token keyword", children: "do" }), " bcftools view ", _jsx(_components.span, { className: "token parameter variable", children: "-S" }), " /home/guoyingwei/project/LeiQiong_cattle2/01.diversity/01.pi/leiqiongguangdong /home/guoyingwei/project/LeiQiong_cattle2/00.data/from_raw_vcf/phased_vcf/chr", _jsx(_components.span, { className: "token variable", children: "${i}" }), ".leiqiong.filtered.snp.maf.phased.vcf.gz ", _jsx(_components.span, { className: "token parameter variable", children: "-Oz" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "-o" }), " /home/guoyingwei/project/LeiQiong_cattle2/03.selection/05.xpehh/guangdong/chr", _jsx(_components.span, { className: "token variable", children: "${i}" }), ".leiqiong.filtered.snp.maf.phased.guangdong.vcf.gz", _jsx(_components.span, { className: "token punctuation", children: ";" }), _jsx(_components.span, { className: "token keyword", children: "done" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 分染色体计算xpehh，支持多线程" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "for" }), " ", _jsx(_components.span, { className: "token for-or-select variable", children: "i" }), " ", _jsx(_components.span, { className: "token keyword", children: "in" }), " ", _jsx(_components.span, { className: "token punctuation", children: "{" }), _jsx(_components.span, { className: "token number", children: "11" }), _jsx(_components.span, { className: "token punctuation", children: ".." }), _jsx(_components.span, { className: "token number", children: "20" }), _jsx(_components.span, { className: "token punctuation", children: "}" }), _jsx(_components.span, { className: "token punctuation", children: ";" }), " ", _jsx(_components.span, { className: "token keyword", children: "do" }), " selscan ", _jsx(_components.span, { className: "token parameter variable", children: "--xpehh" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--vcf" }), " guangdong/chr", _jsx(_components.span, { className: "token variable", children: "${i}" }), ".leiqiong.filtered.snp.maf.phased.guangdong.vcf.gz --vcf-ref hainan/chr", _jsx(_components.span, { className: "token variable", children: "${i}" }), ".leiqiong.filtered.snp.maf.phased.hainan.vcf.gz ", _jsx(_components.span, { className: "token parameter variable", children: "--map" }), " map/leiqiong.filtered.snp.maf.chr", _jsx(_components.span, { className: "token variable", children: "${i}" }), ".map ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " guangdong_hainan.chr", _jsx(_components.span, { className: "token variable", children: "${i}" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--threads" }), " ", _jsx(_components.span, { className: "token number", children: "10" }), _jsx(_components.span, { className: "token punctuation", children: ";" }), " ", _jsx(_components.span, { className: "token keyword", children: "done" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# " }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["norm ", _jsx(_components.span, { className: "token parameter variable", children: "--xpehh" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--files" }), " guangdong_hainan.chr*.xpehh.out --bp-win ", _jsx(_components.span, { className: "token parameter variable", children: "--winsize" }), " ", _jsx(_components.span, { className: "token number", children: "50000" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--log" }), " norm.log\n"] })] }) }), "\n", _jsxs(_components.h2, { id: "矫正后的处理", children: [_jsx(_components.a, { className: "heading-link", href: "#矫正后的处理", 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" }) }) }), "矫正后的处理"] }), "\n", _jsxs(_components.h3, { id: "文件格式", children: [_jsx(_components.a, { className: "heading-link", href: "#文件格式", 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" }) }) }), "文件格式"] }), "\n", _jsx(_components.p, { children: "矫正后会有两种格式的文件：\nxpehh.out.norm和xpehh.out.norm.50kb.windows" }), "\n", _jsx(_components.p, { children: "xpehh.out.norm.50kb.windows输出文件格式：" }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "==> guangdong_hainan.chr10.xpehh.out.norm.50kb.windows <==\n" }), _jsx(_components.span, { className: "code-line", children: "1 50001 70 0 0 5 100 1.93455 -1.22812\n" }), _jsx(_components.span, { className: "code-line", children: "50001 100001 1444 0.066482 0 100 100 3.38201 -1.05993\n" }), _jsx(_components.span, { className: "code-line", children: "100001 150001 1789 0.0134153 0 100 100 2.42656 -1.32729\n" }), _jsx(_components.span, { className: "code-line", children: "150001 200001 748 0.092246 0 100 100 2.79572 -0.331222\n" }), _jsx(_components.span, { className: "code-line", children: "200001 250001 1733 0.0536642 0 100 100 3.5527 -0.975462\n" }), _jsx(_components.span, { className: "code-line", children: "250001 300001 1584 0.00568182 0 100 100 2.2763 -1.32988\n" }), _jsx(_components.span, { className: "code-line", children: "300001 350001 972 0.00102881 0.00102881 100 100 2.01869 -2.07582\n" }), _jsx(_components.span, { className: "code-line", children: "350001 400001 1107 0.00542005 0.00542005 100 100 2.3941 -2.41838\n" }), _jsx(_components.span, { className: "code-line", children: "400001 450001 1273 0.0974077 0 100 100 3.23089 -0.94057\n" }), _jsx(_components.span, { className: "code-line", children: "450001 500001 687 0 0 100 100 1.20025 -1.28854\n" })] }) }), "\n", _jsx(_components.p, { children: "标题行：" }), "\n", _jsx(_components.p, { children: _jsx(_components.code, { className: "language-auto", children: " 2> " }) }), "\n", _jsx(_components.p, { children: "最开始是用这个窗口的结果，最后两列的最大和最小值画图，但感觉不科学，而且不支持overlapped滑动窗口，所以还是用所有位点的，然后网上找到的脚步自己算每个窗口的平均值。" }), "\n", _jsx(_components.p, { children: "xpehh.out.norm文件格式如下：" }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "id pos gpos p1 ihh1 p2 ihh2 xpehh normxpehh crit\n" }), _jsx(_components.span, { className: "code-line", children: "5_31647 31647 0.031647 0.902439 0.000956156 0.97 0.00101616 -0.0264322 0.310865 0\n" }), _jsx(_components.span, { className: "code-line", children: "5_31701 31701 0.031701 0.231707 0.000760266 0.14 0.000923125 -0.0842947 -0.0178511 0\n" }), _jsx(_components.span, { className: "code-line", children: "5_31718 31718 0.031718 0.219512 0.000739398 0.12 0.000924215 -0.0968946 -0.0894309 0\n" }), _jsx(_components.span, { className: "code-line", children: "5_31802 31802 0.031802 0.256098 0.000636091 0.16 0.000840592 -0.121066 -0.226748 0\n" }), _jsx(_components.span, { className: "code-line", children: "5_31805 31805 0.031805 0.292683 0.000636734 0.18 0.000833599 -0.116999 -0.203644 0\n" }), _jsx(_components.span, { className: "code-line", children: "5_31821 31821 0.031821 0.585366 0.000651229 0.77 0.000985299 -0.179834 -0.560608 0\n" })] }) }), "\n", _jsxs(_components.h3, { id: "计算窗口平均值", children: [_jsx(_components.a, { className: "heading-link", href: "#计算窗口平均值", 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" }) }) }), "计算窗口平均值"] }), "\n", _jsx(_components.p, { children: "直接把每条染色体的xpehh.out.norm文件用下面这个python脚本，生成处理后的文件。" }), "\n", _jsx(_components.p, { children: "python脚本如下：" }), "\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: "# XPEHH_win_step.py" }), "\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" }), " click \n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "def" }), " ", _jsx(_components.span, { className: "token function", children: "load_data" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token builtin", children: "file" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" data ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "read_csv", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token builtin", children: "file" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " delimiter", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "\"\\t|\\s+\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" engine", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'python'" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "return" }), " data \n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "def" }), " ", _jsx(_components.span, { className: "token function", children: "results" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "data", _jsx(_components.span, { className: "token punctuation", children: "," }), " step_size", _jsx(_components.span, { className: "token punctuation", children: "," }), " window_size", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" result ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" chromosome_length ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token builtin", children: "max" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "data", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "'pos'" }), _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 keyword", children: "for" }), " BIN_START ", _jsx(_components.span, { className: "token keyword", children: "in" }), " ", _jsx(_components.span, { className: "token builtin", children: "range" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " chromosome_length", _jsx(_components.span, { className: "token punctuation", children: "," }), " step_size", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" BIN_END ", _jsx(_components.span, { className: "token operator", children: "=" }), " BIN_START ", _jsx(_components.span, { className: "token operator", children: "-" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), " ", _jsx(_components.span, { className: "token operator", children: "+" }), " window_size \n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "if" }), " BIN_START ", _jsx(_components.span, { className: "token operator", children: "+" }), " window_size ", _jsx(_components.span, { className: "token operator", children: ">" }), " chromosome_length", _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "break" }), " \n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" normxpehh_vals ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _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: "for" }), " _", _jsx(_components.span, { className: "token punctuation", children: "," }), " row ", _jsx(_components.span, { className: "token keyword", children: "in" }), " data", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "data", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "'pos'" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: ">=" }), " BIN_START", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token operator", children: "&" }), " ", _jsx(_components.span, { className: "token punctuation", children: "(" }), "data", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "'pos'" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "<" }), " BIN_END", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "." }), "iterrows", _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: [" ", _jsx(_components.span, { className: "token keyword", children: "if" }), " ", _jsx(_components.span, { className: "token keyword", children: "not" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "isna", _jsx(_components.span, { className: "token punctuation", children: "(" }), "row", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "'pos'" }), _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: [" normxpehh_vals", _jsx(_components.span, { className: "token punctuation", children: "." }), "append", _jsx(_components.span, { className: "token punctuation", children: "(" }), "row", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "'normxpehh'" }), _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: "# 计算 normxpehh 的平均值并保留4位小数, 统计区间SNP数量 " }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" avg_normxpehh ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token number", children: "0" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" nvar ", _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 keyword", children: "if" }), " ", _jsx(_components.span, { className: "token builtin", children: "len" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "normxpehh_vals", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _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: [" avg_normxpehh ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token builtin", children: "round" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token builtin", children: "sum" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "normxpehh_vals", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token operator", children: "/" }), " ", _jsx(_components.span, { className: "token builtin", children: "len" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "normxpehh_vals", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token number", children: "4" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" nvar ", _jsx(_components.span, { className: "token operator", children: "=" }), " ", _jsx(_components.span, { className: "token builtin", children: "len" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "normxpehh_vals", _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" result", _jsx(_components.span, { className: "token punctuation", children: "." }), "append", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: "[" }), "BIN_START", _jsx(_components.span, { className: "token punctuation", children: "," }), " BIN_END", _jsx(_components.span, { className: "token punctuation", children: "," }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" avg_normxpehh", _jsx(_components.span, { className: "token punctuation", children: "," }), " nvar", _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: "return" }), " result \n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [_jsxs(_components.span, { className: "token decorator annotation punctuation", children: ["@click", _jsx(_components.span, { className: "token punctuation", children: "." }), "command"] }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsxs(_components.span, { className: "token decorator annotation punctuation", children: ["@click", _jsx(_components.span, { className: "token punctuation", children: "." }), "option"] }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'-f'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token string", children: "'--file'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token builtin", children: "help" }), _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'xpehh.out.norm文件，norm后的位点文件，不是区间文件！！'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " required", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "True" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsxs(_components.span, { className: "token decorator annotation punctuation", children: ["@click", _jsx(_components.span, { className: "token punctuation", children: "." }), "option"] }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'-c'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token string", children: "'--chromosome'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token builtin", children: "help" }), _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'染色体号，因为是分染色体做的'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " required", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "True" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsxs(_components.span, { className: "token decorator annotation punctuation", children: ["@click", _jsx(_components.span, { className: "token punctuation", children: "." }), "option"] }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'-w'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token string", children: "'--window'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token builtin", children: "help" }), _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'窗口大小'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token builtin", children: "type" }), _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token builtin", children: "int" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " default", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "50000" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsxs(_components.span, { className: "token decorator annotation punctuation", children: ["@click", _jsx(_components.span, { className: "token punctuation", children: "." }), "option"] }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token string", children: "'-s'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token string", children: "'--step'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token builtin", children: "help" }), _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'步长大小'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token builtin", children: "type" }), _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token builtin", children: "int" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " default", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "50000" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "def" }), " ", _jsx(_components.span, { className: "token function", children: "main" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token builtin", children: "file" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " chromosome", _jsx(_components.span, { className: "token punctuation", children: "," }), " window", _jsx(_components.span, { className: "token punctuation", children: "," }), " step", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" data ", _jsx(_components.span, { className: "token operator", children: "=" }), " load_data", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token builtin", children: "file" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" window_size ", _jsx(_components.span, { className: "token operator", children: "=" }), " window \n"] }), _jsxs(_components.span, { className: "code-line", children: [" step_size ", _jsx(_components.span, { className: "token operator", children: "=" }), " step \n"] }), _jsxs(_components.span, { className: "code-line", children: [" out ", _jsx(_components.span, { className: "token operator", children: "=" }), " results", _jsx(_components.span, { className: "token punctuation", children: "(" }), "data", _jsx(_components.span, { className: "token punctuation", children: "," }), " step_size", _jsx(_components.span, { className: "token punctuation", children: "," }), " window_size", _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: "# 创建一个 DataFrame 对象来保存结果，并使用 to_csv 方法将其写入文件中 " }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [" result_df ", _jsx(_components.span, { className: "token operator", children: "=" }), " pd", _jsx(_components.span, { className: "token punctuation", children: "." }), "DataFrame", _jsx(_components.span, { className: "token punctuation", children: "(" }), "out", _jsx(_components.span, { className: "token punctuation", children: "," }), " columns", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "\"BIN_START\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"BIN_END\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token string", children: "\"avg_normxpehh\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"nvar\"" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" result_df", _jsx(_components.span, { className: "token punctuation", children: "." }), "loc", _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 string", children: "'CHROM'" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), " ", _jsx(_components.span, { className: "token operator", children: "=" }), " chromosome \n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "if" }), " chromosome ", _jsx(_components.span, { className: "token operator", children: "==" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" result_df", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "\"CHROM\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"BIN_START\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"BIN_END\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token string", children: "\"nvar\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"avg_normxpehh\"" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "." }), "to_csv", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsxs(_components.span, { className: "token string-interpolation", children: [_jsx(_components.span, { className: "token string", children: "f'chr" }), _jsxs(_components.span, { className: "token interpolation", children: [_jsx(_components.span, { className: "token punctuation", children: "{" }), "chromosome", _jsx(_components.span, { className: "token punctuation", children: "}" })] }), _jsx(_components.span, { className: "token string", children: ".win.step.mean.XPEHH'" })] }), _jsx(_components.span, { className: "token punctuation", children: "," }), " sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'\\t'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" index", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "False" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token keyword", children: "else" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" result_df", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token string", children: "\"CHROM\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"BIN_START\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"BIN_END\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" ", _jsx(_components.span, { className: "token string", children: "\"nvar\"" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " ", _jsx(_components.span, { className: "token string", children: "\"avg_normxpehh\"" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "." }), "to_csv", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsxs(_components.span, { className: "token string-interpolation", children: [_jsx(_components.span, { className: "token string", children: "f'chr" }), _jsxs(_components.span, { className: "token interpolation", children: [_jsx(_components.span, { className: "token punctuation", children: "{" }), "chromosome", _jsx(_components.span, { className: "token punctuation", children: "}" })] }), _jsx(_components.span, { className: "token string", children: ".win.step.mean.XPEHH'" })] }), _jsx(_components.span, { className: "token punctuation", children: "," }), " sep", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token string", children: "'\\t'" }), _jsx(_components.span, { className: "token punctuation", children: "," }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" index", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token boolean", children: "False" }), _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: ")" }), " \n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "if" }), " __name__ ", _jsx(_components.span, { className: "token operator", children: "==" }), " ", _jsx(_components.span, { className: "token string", children: "'__main__'" }), _jsx(_components.span, { className: "token punctuation", children: ":" }), " \n"] }), _jsxs(_components.span, { className: "code-line", children: [" main", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] })] }) }), "\n", _jsx(_components.p, { children: "生成的文件格式如下：" }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "12 1 50000 14 -0.0586\n" }), _jsx(_components.span, { className: "code-line", children: "12 25001 75000 23 0.2398\n" }), _jsx(_components.span, { className: "code-line", children: "12 50001 100000 206 0.008\n" }), _jsx(_components.span, { className: "code-line", children: "12 75001 125000 536 -0.0816\n" }), _jsx(_components.span, { className: "code-line", children: "12 100001 150000 604 -0.3024\n" }), _jsx(_components.span, { className: "code-line", children: "12 125001 175000 410 -0.5833\n" }), _jsx(_components.span, { className: "code-line", children: "12 150001 200000 298 -0.1776\n" }), _jsx(_components.span, { className: "code-line", children: "12 175001 225000 301 0.348\n" }), _jsx(_components.span, { className: "code-line", children: "12 200001 250000 292 0.4825\n" }), _jsx(_components.span, { className: "code-line", children: "12 225001 275000 279 0.1246\n" })] }) }), "\n", _jsx(_components.p, { children: "把他们cat到一起就可以画图了。" })] }); } function MDXContent(props = {}) { const {wrapper: MDXLayout} = { ..._provideComponents(), ...props.components }; return MDXLayout ? _jsx(MDXLayout, { ...props, children: _jsx(_createMdxContent, { ...props }) }) : _createMdxContent(props); } return { default: MDXContent };