From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 26 Mar 2011 05:54:18 +0000 (+0000)
Subject: Edited wiki page PhyloBioRuby through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=84059f1404831b2fb25684f982c25fef673c9b16;p=jalview.git

Edited wiki page PhyloBioRuby through web user interface.
---

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index ab6faf9..c6e7f59 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -43,27 +43,29 @@ msa.each do |entry|
 end
 }}}
 
-Blah
+The following example shows how to read in a *FASTA*-formatted multiple sequence file.
 {{{
-# Reads in a Fasta-formatted multiple sequence alignment (which does
+#!/usr/bin/env ruby
+require 'bio'
+
+# 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 = Bio::Alignment::MultiFastaFormat.new(File.open('infile.fasta').read)
 fasta_seqs.entries.each do |seq|
-  seq_ary.push( 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 }
+seqs = Bio::Alignment.new(seq_ary)
 
-
-puts seqs.consensus
+# Prints each sequence to the console.
+seqs.each { |seq| puts seq.to_s }
 
 # Writes multiple sequence alignment (possibly unaligned) 'seqs'
-# to a file in phylip format.
+# to a file in PHYLIP format.
 File.open('out1.phylip', 'w') do |f|
   f.write(seqs.output(:phylip))
 end