{"id":5719,"date":"2020-03-01T07:14:38","date_gmt":"2020-03-01T07:14:38","guid":{"rendered":"http:\/\/41j.com\/blog\/?p=5719"},"modified":"2020-03-01T07:14:44","modified_gmt":"2020-03-01T07:14:44","slug":"quick-script-to-download-uniprot-info-for-proteins-from-pfam-trees-newick-tree-format","status":"publish","type":"post","link":"https:\/\/41j.com\/blog\/2020\/03\/quick-script-to-download-uniprot-info-for-proteins-from-pfam-trees-newick-tree-format\/","title":{"rendered":"Quick script to download Uniprot info for proteins from Pfam trees (Newick tree format)"},"content":{"rendered":"<div class=\"wp-block-syntaxhighlighter-code \"><pre class=\"brush: plain; title: ; notranslate\" title=\"\">\nfrom ete3 import Tree\nimport sys\nimport os\nimport urllib.request\n\nt = Tree(sys.argv&#x5B;1])\n\nfor l in t:\n        id = l.name.split(&quot;\/&quot;)&#x5B;0]\n        print(f&quot;Accession: {id}&quot;)\n        if os.path.exists(f&quot;{id}.txt&quot;) == False:\n                print(&quot;Downloading...&quot;)\n                page = urllib.request.urlopen(f&quot;https:\/\/www.uniprot.org\/uniprot\/{id}.txt&quot;)\n\n                out_file = open(f&quot;{id}.txt&quot;,&quot;wb&quot;)\n                out_file.write(page.read())\n                out_file.close()\n\n<\/pre><\/div>","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-5719","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p1RRoU-1uf","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/5719","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/comments?post=5719"}],"version-history":[{"count":2,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/5719\/revisions"}],"predecessor-version":[{"id":5721,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/5719\/revisions\/5721"}],"wp:attachment":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/media?parent=5719"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/categories?post=5719"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/tags?post=5719"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}