{"id":1877,"date":"2025-07-19T20:38:49","date_gmt":"2025-07-19T12:38:49","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1877"},"modified":"2025-07-19T21:00:38","modified_gmt":"2025-07-19T13:00:38","slug":"jcvi%e8%bf%9b%e8%a1%8c%e5%be%ae%e5%85%b1%e7%ba%bf%e6%80%a7%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/07\/19\/jcvi%e8%bf%9b%e8%a1%8c%e5%be%ae%e5%85%b1%e7%ba%bf%e6%80%a7%e5%88%86%e6%9e%90\/","title":{"rendered":"JCVI\u8fdb\u884c\u5fae\u5171\u7ebf\u6027\u5206\u6790"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1877\" class=\"elementor elementor-1877\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-a93519e e-flex e-con-boxed e-con e-parent\" data-id=\"a93519e\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-bdd9ccc elementor-widget elementor-widget-heading\" data-id=\"bdd9ccc\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. \u4e0b\u8f7d\u8f6f\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ba46cd1 elementor-widget elementor-widget-code-highlight\" data-id=\"ba46cd1\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>git clone https:\/\/github.com\/tanghaibao\/jcvi.git\ncd jcvi\nconda env create -f environment.yml<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f2ede81 elementor-widget elementor-widget-heading\" data-id=\"f2ede81\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. \u51c6\u5907\u8f93\u5165\u6587\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b621bf3 elementor-widget elementor-widget-text-editor\" data-id=\"b621bf3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u5c06gff\u6587\u4ef6\u8f6c\u6362\u4e3ajcvi\u6307\u5b9a\u7684bed\u6587\u4ef6\uff0c\u6211\u5728\u7ec3\u4e60\u7684\u65f6\u5019\u662f\u75283\u4e2a\u7269\u79cd\u8fdb\u884c\u8054\u7cfb\uff0c\u6240\u4ee5\u540e\u7eed\u7684\u4ee3\u7801\u90fd\u662f\u4ee5\u8fd9\u4e09\u4e2a\u7269\u79cd\u7684\u5fae\u5171\u7ebf\u6027\u5206\u6790\u8fdb\u884c\u7684\/<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5207eec elementor-widget elementor-widget-code-highlight\" data-id=\"5207eec\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>python3 -m jcvi.formats.gff bed --type=mRNA Bsap.gff -o Bsap.bed\npython3 -m jcvi.formats.gff bed --type=mRNA Daod.gff -o Daod.bed\npython3 -m jcvi.formats.gff bed --type=mRNA Dcul.gff -o Dcul.bed<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-19f2299 elementor-widget elementor-widget-heading\" data-id=\"19f2299\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. \u5fae\u5171\u7ebf\u6027\u5206\u6790<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0f25ca0 elementor-widget elementor-widget-heading\" data-id=\"0f25ca0\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.1 \u9274\u5b9a\u5171\u7ebf\u6027\u533a\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-13d5197 elementor-widget elementor-widget-text-editor\" data-id=\"13d5197\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u6ce8\uff1a\u8981\u9009\u5b9a\u4e00\u4e2a\u53c2\u8003\u7269\u79cd\uff0c\u968f\u540e\u5176\u4ed6\u7269\u79cd\u5747\u4e0e\u53c2\u8003\u7269\u79cd\u9274\u5b9a\u5171\u7ebf\u6027\u533a\u5757\uff0c\u672c\u6b21\u9009\u62e9\u7684\u662fDaod\u8fd9\u4e2a\u7269\u79cd\u3002\u6b64\u5916\uff0c\u8fd9\u4e00\u6b65\u8f93\u5165\u6587\u4ef6\u5fc5\u987b\u662f\u5728\u5f53\u524d\u6587\u4ef6\u4e0b\u53ef\u4ee5\u76f4\u63a5\u627e\u5230\u7684.cds\u548c.bed\u6587\u4ef6\u7684\uff0c\u4f8b\u5982\u8f93\u5165\u7684Daod\uff0c\u8f6f\u4ef6\u5c31\u4f1a\u5728\u5f53\u524d\u6587\u4ef6\u5939\u5bfb\u627eDaod.cds\u548cDaod.bed.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-63bef94 elementor-widget elementor-widget-code-highlight\" data-id=\"63bef94\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>python3 -m jcvi.compara.catalog ortholog Daod Bsap --no_strip_names\npython3 -m jcvi.compara.catalog ortholog Daod Dcul --no_strip_names<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b756609 elementor-widget elementor-widget-heading\" data-id=\"b756609\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.2 \u63d0\u53d61\u5bf91\u7684\u5171\u7ebf\u6027\u533a\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8c84880 elementor-widget elementor-widget-code-highlight\" data-id=\"8c84880\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>python -m jcvi.compara.synteny mcscan Daod.bed Daod.Bsap.lifted.anchors --iter=1 -o Daod.Bsap.block\npython -m jcvi.compara.synteny mcscan Daod.bed Daod.Dcul.lifted.anchors --iter=1 -o Daod.Dcul.block<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3ecdf6d elementor-widget elementor-widget-heading\" data-id=\"3ecdf6d\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.3 \u5408\u5e76\u591a\u4e2a\u7269\u79cd\u548c\u53c2\u8003\u7269\u79cd\u7684\u5171\u7ebf\u6027\u533a\u5757\u6587\u4ef6<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3d0f44c elementor-widget elementor-widget-code-highlight\" data-id=\"3d0f44c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>paste Daod.Bsap.block Daod.Dcul.block|cut -f 1,2,4 > Combine.block<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-99c87de elementor-widget elementor-widget-heading\" data-id=\"99c87de\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.4 \u63d0\u53d6\u76ee\u7684\u57fa\u56e0\u53ca\u5176\u524d\u540e5\u4e2a\u57fa\u56e0<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-17d79b7 elementor-widget elementor-widget-code-highlight\" data-id=\"17d79b7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>grep -C 5 \"Daodo07aG0604400\" Combine.block > Daodo07aG0604400.block<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f948fe4 elementor-widget elementor-widget-heading\" data-id=\"f948fe4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.5 \u5408\u5e76\u6240\u6709\u7684bed\u6587\u4ef6<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c1932ff elementor-widget elementor-widget-code-highlight\" data-id=\"c1932ff\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>python -m jcvi.formats.bed merge Daod.bed Bsap.bed Dcul.bed -o Combine.bed<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-96ab986 elementor-widget elementor-widget-heading\" data-id=\"96ab986\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">3.6 \u7ed8\u5236\u5fae\u5171\u7ebf\u6027\u56fe<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-51e9765 elementor-widget elementor-widget-code-highlight\" data-id=\"51e9765\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>python -m jcvi.graphics.synteny Daodo07aG0604400.block Combine.bed block.layout --outputprefix Daodo07aG0604400<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a79f75f elementor-widget elementor-widget-text-editor\" data-id=\"a79f75f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u4ee5\u4e0b\u4e3a\u914d\u7f6e\u6587\u4ef6\u201cblock.layout\u201d\u7684\u683c\u5f0f<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-31e919b elementor-widget elementor-widget-code-highlight\" data-id=\"31e919b\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp> x,   y, rotation,   ha,     va,   color, ratio,            label\n0.5, 0.6,        0, left, center,       m,     1,       Daod\n0.5, 0.4,        0, left, center, #fc8d62,     1,       Bsap\n0.5, 0.2,        0, left, center, red,     1,       Dcul\n# edges\ne, 0, 1\ne, 1, 2<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1867b05 elementor-widget elementor-widget-image\" data-id=\"1867b05\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"1024\" height=\"572\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/07\/\u5fae\u4fe1\u622a\u56fe_20250719205729-1024x572.jpg\" class=\"attachment-large size-large wp-image-1885\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/07\/\u5fae\u4fe1\u622a\u56fe_20250719205729-1024x572.jpg 1024w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/07\/\u5fae\u4fe1\u622a\u56fe_20250719205729-300x167.jpg 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/07\/\u5fae\u4fe1\u622a\u56fe_20250719205729-768x429.jpg 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/07\/\u5fae\u4fe1\u622a\u56fe_20250719205729-1536x858.jpg 1536w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/07\/\u5fae\u4fe1\u622a\u56fe_20250719205729.jpg 1553w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" 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