{"id":1333,"date":"2023-11-21T10:54:12","date_gmt":"2023-11-21T10:54:12","guid":{"rendered":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1333"},"modified":"2024-05-08T15:10:29","modified_gmt":"2024-05-08T15:10:29","slug":"pgap%e5%ae%89%e8%a3%9d%e7%ad%86%e8%a8%98","status":"publish","type":"post","link":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1333","title":{"rendered":"PGAP\u5b89\u88dd\u7b46\u8a18"},"content":{"rendered":"\n<h4 class=\"wp-block-heading\">2023 by RY Li <\/h4>\n\n\n\n<p>PGAP github\u9023\u7d50\uff1a<a href=\"https:\/\/github.com\/ncbi\/pgap\/wiki\" data-type=\"URL\" data-id=\"https:\/\/github.com\/ncbi\/pgap\/wiki\">https:\/\/github.com\/ncbi\/pgap\/wiki<\/a><\/p>\n\n\n\n<!--more-->\n\n\n\n<h3 class=\"wp-block-heading\">\u904b\u884cPGAP\u524d\u9700\u8981\u4ee5\u4e0b\u689d\u4ef6\uff1a<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Python (version 3.6 or higher)<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>the ability to run Docker (see&nbsp;<a href=\"https:\/\/docs.docker.com\/install\/\">https:\/\/docs.docker.com\/install\/<\/a>&nbsp;if it is not already installed), Singularity, or Podman<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>about 100GB of storage for the supplemental data and working space<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>and 2GB-4GB of memory available per CPU used by your container.<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The CPU must have SSE 4.2 support (released in 2008).<\/li>\n<\/ul>\n\n\n\n<p>\u5c07PGAP \u5b89\u88dd\u65bcZ2\u5de5\u4f5c\u7ad9\uff0c\u4f5c\u696d\u7cfb\u7d71\u662fUbuntu\uff0c\u4e26\u5df2\u7d93\u5b89\u88dd\u597dPython \u53ca <a href=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1298\" data-type=\"URL\" data-id=\"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1298\">Singularity<\/a> (\u53c3\u7167CulebrONT\u5b89\u88dd\u7b46\u8a18)\uff1a<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Download<\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code>$ wget -O pgap.py https:\/\/github.com\/ncbi\/pgap\/raw\/prod\/scripts\/pgap.py<\/code><\/pre>\n\n\n\n<p>\u9ed8\u8a8d\u60c5\u6cc1\u4e0b\uff0c\u65bc\u5bb6\u76ee\u9304 <code>$home<\/code> \u4e0b\u6703\u6709 <code>pgap.py <\/code>\u6a94\u6848<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ chmod +x pgap.py<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code>$ .\/pgap.py --update<\/code><\/pre>\n\n\n\n<p>\u6a94\u6848\u6709\u5f88\u5927\u8981\u4e0b\u8f09\u4e00\u9663\u5b50 \u5bb6\u76ee\u9304\u6703\u51fa\u73fe <code>.pgap<\/code> \u7684\u8cc7\u6599\u593e\uff0c\u9019\u6a23\u5c31\u5b89\u88dd\u5b8c\u6210\u4e86\uff5e\u7c21\u55ae\u5504<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">\u6e2c\u8a66\u5b89\u88dd<\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code>$ .\/pgap.py -r -o mg37_results -g .\/pgap\/test_genome\/MG37\/ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitalium'<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\u8a3b\u89e3\u81ea\u5df1\u7684fasta\u6a94\u6848<\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code>$ .\/pgap.py -r -o &lt;results&gt; -g &lt;fasta&gt; -s '&lt;organism_name&gt;'<\/code><\/pre>\n\n\n\n<p>\u5982\u679c\u4e0d\u78ba\u5b9a\u7269\u7a2e\u540d\u7a31 (organism_name)\uff0c\u53ef\u4ee5\u586b\u4e0a\u6709\u53ef\u80fd\u7684\u7269\u7a2e\u540d\u7a31\uff0c<\/p>\n\n\n\n<p>\u5728\u52a0\u4e0a <code>--taxcheck<\/code> \u8ddf &#8211;<code>-auto-correct-tax<\/code>\uff0c\u5c31\u6703\u81ea\u52d5\u9032\u884c ANI \u5206\u6790\u4e26\u4f9d\u64daANI\u7269\u7a2e\u9451\u5b9a\u7684\u7d50\u679c\u9032\u884c\u8a3b\u89e3\u5594<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ .\/pgap.py -r -o &lt;results&gt; -g &lt;fasta&gt; --taxcheck --auto-correct-tax -s '&lt;organism_name&gt;'\n<\/code><\/pre>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\u53e6\u5916\u6211\u8acbChatGPT\u5e6b\u6211\u5beb\u4e86\u4e00\u500b\u7c21\u55ae\u7684 script\uff0c\u53ef\u4ee5\u4e00\u6b21\u8a3b\u89e3\u591a\u500b\u6a23\u672c\uff1a<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>#!\/bin\/bash\n\nfor sample in {01..12}; do\n    .\/pgap.py -r -o \"MRSA_${sample}_results_ANI\" -g \"\/home\/onion\/112_wgs_data\/MRSA_assembly\/${sample}\/assembly.fasta\" --taxcheck -s 'Staphylococcus aureus'\ndone<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>2023 by RY Li PGAP github\u9023\u7d50\uff1ahttps:\/\/github.com\/ncbi\/pgap\/wiki<\/p>\n","protected":false},"author":5,"featured_media":1696,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"colormag_page_container_layout":"default_layout","colormag_page_sidebar_layout":"default_layout","footnotes":""},"categories":[5],"tags":[15,14,18],"class_list":["post-1333","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-blog","tag-bioinformatics","tag-genomics","tag-linux"],"magazineBlocksPostFeaturedMedia":{"thumbnail":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-150x150.jpg","medium":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-300x225.jpg","medium_large":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-768x576.jpg","large":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-1024x768.jpg","1536x1536":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-1536x1152.jpg","2048x2048":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1.jpg","colormag-highlighted-post":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-392x272.jpg","colormag-featured-post-medium":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-390x205.jpg","colormag-featured-post-small":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-130x90.jpg","colormag-featured-image":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-800x445.jpg","colormag-default-news":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-150x150.jpg","colormag-featured-image-large":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-1400x600.jpg"},"magazineBlocksPostAuthor":{"name":"member","avatar":"https:\/\/secure.gravatar.com\/avatar\/60eb10659d1084a90395612fe5ec63ad02f2ea36b9e5c86a8f2240354e259640?s=96&d=mm&r=g"},"magazineBlocksPostCommentsNumber":false,"magazineBlocksPostExcerpt":"2023 by RY Li PGAP github\u9023\u7d50\uff1ahttps:\/\/github.com\/ncbi\/pgap\/wiki","magazineBlocksPostCategories":["blog"],"magazineBlocksPostViewCount":189,"magazineBlocksPostReadTime":1,"magazine_blocks_featured_image_url":{"full":["https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1.jpg",1600,1200,false],"medium":["https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-300x225.jpg",300,225,true],"thumbnail":["https:\/\/megagenome.nchu.edu.tw\/wordpress\/wp-content\/uploads\/2024\/05\/blogheader-1-150x150.jpg",150,150,true]},"magazine_blocks_author":{"display_name":"member","author_link":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?author=5"},"magazine_blocks_comment":0,"magazine_blocks_author_image":"https:\/\/secure.gravatar.com\/avatar\/60eb10659d1084a90395612fe5ec63ad02f2ea36b9e5c86a8f2240354e259640?s=96&d=mm&r=g","magazine_blocks_category":"<a href=\"#\" class=\"category-link category-link-5\">blog<\/a>","_links":{"self":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/1333","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1333"}],"version-history":[{"count":8,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/1333\/revisions"}],"predecessor-version":[{"id":1428,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/1333\/revisions\/1428"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=\/wp\/v2\/media\/1696"}],"wp:attachment":[{"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1333"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1333"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1333"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}