{"id":445,"date":"2017-02-08T22:12:26","date_gmt":"2017-02-08T21:12:26","guid":{"rendered":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/?p=445"},"modified":"2017-02-08T22:17:11","modified_gmt":"2017-02-08T21:17:11","slug":"alignment-nex2phy-few-liner","status":"publish","type":"post","link":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/2017\/02\/08\/alignment-nex2phy-few-liner\/","title":{"rendered":"Alignment Nex2Phy few-liner"},"content":{"rendered":"<p><strong>Alignment file format conversion for the efficient<\/strong><\/p>\n<p>Today, I needed to convert a series of alignments, which were stored in the common <em>nexus<\/em> format, into <em>newick<\/em> format. In order to do this efficiently, I wrote the following few-liner.<\/p>\n<div style=\"background-color: #ffebdb\">\n<p style=\"padding-left: 30px\"><code>#!\/usr\/bin\/env python2.7<br \/>\nimport sys<br \/>\nfrom Bio import AlignIO<br \/>\ninFn = sys.argv[1]<br \/>\ninp = open(inFn, 'rU')<br \/>\noutp = open(inFn+'.phy', 'w')<br \/>\naln = AlignIO.parse(inp, 'nexus')<br \/>\nAlignIO.write(aln, outp, 'phylip')<br \/>\noutp.close()<br \/>\ninp.close()<br \/>\n<\/code><\/p>\n<\/div>\n<p>The above-code is very ordinary and great to have handy.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Alignment file format conversion for the efficient Today, I needed to convert a series of alignments, which were stored in the common nexus format, into newick format. In order to do this efficiently, I wrote the following few-liner. #!\/usr\/bin\/env python2.7 import sys from Bio import AlignIO inFn = sys.argv[1] inp = open(inFn, &#8216;rU&#8217;) outp = [&hellip;]<\/p>\n","protected":false},"author":2306,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[57598],"tags":[],"class_list":["post-445","post","type-post","status-publish","format-standard","hentry","category-bioinformatics"],"_links":{"self":[{"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/posts\/445","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=445"}],"version-history":[{"count":6,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/posts\/445\/revisions"}],"predecessor-version":[{"id":451,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/posts\/445\/revisions\/451"}],"wp:attachment":[{"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/media?parent=445"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/categories?post=445"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.fu-berlin.de\/gruenstaeudl\/wp-json\/wp\/v2\/tags?post=445"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}