{"id":693,"date":"2018-11-08T18:54:49","date_gmt":"2018-11-08T17:54:49","guid":{"rendered":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/?p=693"},"modified":"2018-11-08T18:57:35","modified_gmt":"2018-11-08T17:57:35","slug":"commandline-search-interface-for-ena","status":"publish","type":"post","link":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/2018\/11\/08\/commandline-search-interface-for-ena\/","title":{"rendered":"Commandline search interface for ENA"},"content":{"rendered":"<p><strong>Digging through ENA records.<\/strong><\/p>\n<p>By using the Python library <a href=\"http:\/\/joss.theoj.org\/papers\/10.21105\/joss.00418\" target=\"_blank\" rel=\"noopener\">enasearch<\/a>, which provides a Python-based interaction with ENA&#8217;s API, commandline searches of the ENA databases have become a delight.<\/p>\n<p>Take, for example, the aim to infer the number of individual accessions of the common plant DNA barcoding marker <em>trnK-matK<\/em> that have become available over the course of the year 2017. This very specific aim can be achieved via the following command:<\/p>\n<div style=\"background-color: #ffebdb\">\n<pre>enasearch search_data \\\r\n--query 'organelle=plastid \\\r\nAND (first_public&gt;2017-01-01 AND first_public&lt;2018-01-01) \\\r\nAND (description=\"*matK*\" OR description=\"*maturase K*\") \\\r\nAND (description=\"*trnK*\" OR description=\"*tRNA-Lys*\") \\\r\nAND tax_division=PLN AND topology=LINEAR' \\\r\n--result sequence_release --display report | wc -l\r\n<\/pre>\n<\/div>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Digging through ENA records. By using the Python library enasearch, which provides a Python-based interaction with ENA&#8217;s API, commandline searches of the ENA databases have become a delight. Take, for example, the aim to infer the number of individual accessions of the common plant DNA barcoding marker trnK-matK that have become available over the course [&hellip;]<\/p>\n","protected":false},"author":2306,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9],"tags":[],"class_list":["post-693","post","type-post","status-publish","format-standard","hentry","category-allgemein"],"_links":{"self":[{"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/posts\/693","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/users\/2306"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/comments?post=693"}],"version-history":[{"count":4,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/posts\/693\/revisions"}],"predecessor-version":[{"id":697,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/posts\/693\/revisions\/697"}],"wp:attachment":[{"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/media?parent=693"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/categories?post=693"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/tags?post=693"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}