{"id":128,"date":"2021-10-26T23:26:12","date_gmt":"2021-10-26T15:26:12","guid":{"rendered":"https:\/\/linguopeng.top\/?p=128"},"modified":"2022-01-18T16:48:09","modified_gmt":"2022-01-18T08:48:09","slug":"picrust1-%e5%88%862%ef%bc%8c3%e7%ba%a7%e6%97%b6","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=128","title":{"rendered":"picrust1-\u52062\uff0c3\u7ea7\u65f6"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>#\u6fc0\u6d3b\u73af\u5883\nconda activate qiime2-2019.7\n#\u6309\u62f7\u8d1d\u6570\u6807\u51c6\u5316OTU\u8868\uff0c\u5904\u7406\u81ea\u5df1\u6570\u636e\u6210picrust1\u6240\u9700\n##\u5b89\u88c5\u597dqiime2\uff0c\u7136\u540e\u5bfc\u5165\u6210qiime2\u683c\u5f0f\uff0c\u65b9\u4fbf\u540e\u9762\u4f7f\u7528\n#feature-table.biom\u6587\u4ef6\n#qiime tools import   --input-path ..\/97_otus.fasta --output-path ref-sequences.qza --type 'FeatureData&#91;Sequence]' \\\nqiime vsearch cluster-features-closed-reference --i-sequences rep-seqs.qza --output-dir closed-ref-otu\/ --i-table table.qza --i-reference-sequences ref-sequences.qza   --p-perc-identity 0.97 \nqiime tools export --input-path closed-ref-otu\/clustered_table.qza --output-path closed-ref-otu\n#\u6fc0\u6d3b\u73af\u5883\nconda activate picrust1\n#biom convert -i otu_table.biom -o otu_table_json.biom --to-json\n#normalize_by_copy_number.py -i otu_table_json.biom -o normalized_otus.biom\n#\u6309\u62f7\u8d1d\u6570\u6807\u51c6\u5316OTU\u8868\uff0c\u5904\u7406\u81ea\u5df1\u6570\u636e\u6210picrust1\u6240\u9700\nnormalize_by_copy_number.py -i closed-ref-otu\/feature-table.biom -o normalized_otus.biom\n#biom convert --to-tsv -i closed-ref-otu\/feature-table.biom -o closed_reference_otu_table.tsv\n#normalize_by_copy_number.py -i feature-table.biom -o normalized_otus.biom\n#\u9884\u6d4b\u5b8f\u57fa\u56e0\u7ec4\npredict_metagenomes.py -i normalized_otus.biom -o metagenome_predictions.biom\n# \u8f6c\u6362\u683c\u5f0f\u4e3atxt\nbiom convert -i metagenome_predictions.biom -o metagenome_predictions.txt --table-type=\"OTU table\" --to-tsv\n#\u8c03\u6574\u4e3a\u6807\u51c6\u8868\u683c\n#sed -i '\/# Const\/d;s\/#OTU \/\/g' metagenome_predictions.txt \u6211\u662f\u9ed1\u82f9\u679c\uff0c\u53ef\u80fdmac sed\u547d\u4ee4\u6709\u6240\u5dee\u522b\uff0c\u6ca1\u6709#\u5b8c\u6210\u8fd9\u4e2a\u547d\u4ee4\u3002\n#\u6309\u529f\u80fd\u7ea7\u522b\u5206\u7c7b\u6c47\u603b\uff0c-c\u6307\u8f93\u51fa\u7c7b\u578b\uff0c\u6709KEGG_Pathways, COG_Category\uff0cRFAM\u4e09\u79cd\uff0c-l\u662f\u7ea7\u522b\uff0c\u52063\u7ea7\ncategorize_by_function.py -i metagenome_predictions.biom -c KEGG_Pathways -l 3 -o metagenome_predictions.L3.biom\n#summarize_taxa.py -i metagenome_predictions.L3.biom -o sum_taxa_level3\/ --absolute_abundance --md_identifier #\"KEGG_Pathways\" --level 3\n# \u8f6c\u6362\u683c\u5f0f\u4e3atxt\uff0c\u7136\u540e\u5c31\u53ef\u4ee5\u770b\u7ed3\u679c\u4e86\uff0c\u4f7f\u7528excel\u6253\u5f00\u5373\u53ef\u6e05\u695a\u67e5\u770b\u3002\nbiom convert -i metagenome_predictions.L3.biom -o metagenome_predictions.L3.txt --table-type=\"OTU table\" --to-tsv\n#\u540c\u6837\u6ca1\u6709\u5b8c\u6210 sed -i '\/# Const\/d;s\/#OTU \/\/g' metagenome_predictions.L3.txt\n#\u6309\u529f\u80fd\u7ea7\u522b\u5206\u7c7b\u6c47\u603b\uff0c-c\u6307\u8f93\u51fa\u7c7b\u578b\uff0c\u6709KEGG_Pathways, COG_Category\uff0cRFAM\u4e09\u79cd\uff0c-l\u662f\u7ea7\u522b\uff0c2\u7ea7\u65f6\ncategorize_by_function.py -i metagenome_predictions.biom -c KEGG_Pathways -l 2 -o metagenome_predictions.L2.biom\n# \u8f6c\u6362\u683c\u5f0f\u4e3atxt\uff0c\u7136\u540e\u5c31\u53ef\u4ee5\u770b\u7ed3\u679c\u4e86\uff0c\u4f7f\u7528excel\u6253\u5f00\u5373\u53ef\u6e05\u695a\u67e5\u770b\u3002\nbiom convert -i metagenome_predictions.L2.biom -o metagenome_predictions.L2.txt --table-type=\"OTU table\" --to-tsv\n\n#\u6548\u679cLi S, You J, Wang Z, Liu Y, Wang B, Du M, Zou T. Curcumin alleviates high-fat diet-induced hepatic steatosis and obesity in association with modulation of gut microbiota in mice. Food Res Int. 2021 May;143:110270. doi: 10.1016\/j.foodres.2021.110270<span title=\"DOI: 10.1016\/j.foodres.2021.110270\" class=\"es-webpage-collect main\" es-id-type=\"DOI\" es-id=\"10.1016\/j.foodres.2021.110270\" es-collect-button-id=\"0\" style=\"cursor: pointer; padding: 0px 0.15em; border-radius: 0.65em;\"><svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 1000 1000\" enable-background=\"new 0 0 1000 1000\" xml:space=\"preserve\" height=\"1em\">\n        <g><path d=\"M852.3,135.6l-47.7,48.3c157.6,178.7,157.4,451,0.1,631l48.8,49.5C1035.9,672.1,1035.5,327.2,852.3,135.6z M740.9,248.6l-49.3,49.9c96.1,115.5,96.1,285.8,0.5,402.1l48.8,49.6C863.4,606.1,863.6,391.5,740.9,248.6z M195.4,183.9l-47.7-48.3c-183.2,191.6-183.6,536.5-1.2,728.8l48.8-49.5C37.9,635,37.8,362.6,195.4,183.9z M259.1,248.6C136.4,391.5,136.6,606.1,259,750.3l48.8-49.6c-95.6-116.4-95.6-286.6,0.4-402.1L259.1,248.6z M499.8,340.4c-87.3,0-158.1,71.8-158.1,160.4c0,88.5,70.8,160.4,158.1,160.4c87.3,0,158.1-71.8,158.1-160.4C657.8,412.2,587,340.4,499.8,340.4z\" style=\"fill: rgb(32, 85, 138);\"><\/g>\n        <\/svg><\/span>. Epub 2021 Mar 9. PMID: 33992371<span title=\"PMID: 33992371\" class=\"es-webpage-collect main\" es-id-type=\"PMID\" es-id=\"33992371\" es-collect-button-id=\"1\" style=\"cursor: pointer; padding: 0px 0.15em; border-radius: 0.65em;\"><svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 1000 1000\" enable-background=\"new 0 0 1000 1000\" xml:space=\"preserve\" height=\"1em\">\n        <g><path d=\"M852.3,135.6l-47.7,48.3c157.6,178.7,157.4,451,0.1,631l48.8,49.5C1035.9,672.1,1035.5,327.2,852.3,135.6z M740.9,248.6l-49.3,49.9c96.1,115.5,96.1,285.8,0.5,402.1l48.8,49.6C863.4,606.1,863.6,391.5,740.9,248.6z M195.4,183.9l-47.7-48.3c-183.2,191.6-183.6,536.5-1.2,728.8l48.8-49.5C37.9,635,37.8,362.6,195.4,183.9z M259.1,248.6C136.4,391.5,136.6,606.1,259,750.3l48.8-49.6c-95.6-116.4-95.6-286.6,0.4-402.1L259.1,248.6z M499.8,340.4c-87.3,0-158.1,71.8-158.1,160.4c0,88.5,70.8,160.4,158.1,160.4c87.3,0,158.1-71.8,158.1-160.4C657.8,412.2,587,340.4,499.8,340.4z\" style=\"fill: rgb(32, 85, 138);\"><\/g>\n        <\/svg><\/span>.\n<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full is-style-default\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/1-1.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"1067\" height=\"982\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/10\/1-1.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-129\"\/><\/div><\/figure>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[3],"class_list":["post-128","post","type-post","status-publish","format-standard","hentry","category-r","tag-r"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/128","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=128"}],"version-history":[{"count":3,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/128\/revisions"}],"predecessor-version":[{"id":268,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/128\/revisions\/268"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=128"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=128"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=128"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}