From 0a133c612b5c1acc1436a94b0d65af27dd4bba42 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 26 Mar 2011 05:49:18 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index 503fc75..ab6faf9 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -43,6 +43,32 @@ msa.each do |entry| end }}} +Blah +{{{ +# Reads in a Fasta-formatted multiple sequence alignment (which does +# not have to be aligned, though) and stores its sequences in +# array 'seq_ary'. +seq_ary = Array.new +fasta_seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read) +fasta_seqs.entries.each do |seq| + seq_ary.push( seq ) +end + +# Creates a multiple sequence alignment (possibly unaligned) named +# 'seqs' from array 'seq_ary'. +seqs = Bio::Alignment.new( seq_ary ) +seqs.each { |seq| puts seq.to_s } + + +puts seqs.consensus + +# Writes multiple sequence alignment (possibly unaligned) 'seqs' +# to a file in phylip format. +File.open('out1.phylip', 'w') do |f| + f.write(seqs.output(:phylip)) +end +}}} + Relevant API documentation: * [http://bioruby.open-bio.org/rdoc/classes/Bio/ClustalW/Report.html Bio::ClustalW::Report] -- 1.7.10.2