From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 26 Mar 2011 06:16:06 +0000 (+0000)
Subject: Edited wiki page PhyloBioRuby through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3bf089107c5c3b94f513664fb59e3d0563c6a8d4;p=jalview.git

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

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index a3be960..b693825 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -25,14 +25,37 @@ Copyright (C) 2011 Christian M Zmasek. All rights reserved.
 
 This automatically determines the format
 {{{
+#!/usr/bin/env ruby
+require 'bio'
+
+seq_ary = Array.new
 ff = Bio::FlatFile.auto('bcl2.fasta')
 ff.each_entry do |entry|
-  puts entry.entry_id          # identifier of the entry
-  puts entry.definition        # definition of the entry
-  puts entry.seq               # sequence data of the entry
+  seq_ary.push(entry)
+  puts entry.entry_id          # prints the identifier of the entry
+  puts entry.definition        # prints the definition of the entry
+  puts entry.seq               # prints the sequence data of the entry
+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 }
+
+# Writes multiple sequence alignment (possibly unaligned) 'seqs'
+# to a file in PHYLIP format.
+File.open('out0.phylip', 'w') do |f|
+  f.write(seqs.output(:phylip))
+end
+
+# Writes multiple sequence alignment (possibly unaligned) 'seqs'
+# to a file in FASTA format.
+File.open('out0.fasta', 'w') do |f|
+  f.write(seqs.output(:fasta))
 end
 }}}
 
+
 ==== ClustalW Format ====
 
 The following example shows how to read in a *ClustalW*-formatted multiple sequence alignment.