JAL-2805 JAL-2847 JAL-281 getTreeFile made public

[jalview.git] / wiki / PhyloBioRuby.wiki

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 0bd30f5..4b6b45f 100644 (file)
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -10,7 +10,7 @@ Tutorial for multiple sequence alignments and phylogenetic methods in [http://bi
 
 Eventually, this is expected to be placed on the official !BioRuby page.
 
-Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
+Author: [https://sites.google.com/site/cmzmasek/ Christian Zmasek], Sanford-Burnham Medical Research Institute
 
  
 Copyright (C) 2011 Christian M Zmasek. All rights reserved.
@@ -23,6 +23,39 @@ Copyright (C) 2011 Christian M Zmasek. All rights reserved.
 
 === Reading in a Multiple Sequence Alignment from a File ===
 
+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|
+  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.
@@ -81,6 +114,13 @@ Relevant API documentation:
  * [http://bioruby.open-bio.org/rdoc/classes/Bio/Alignment.html Bio::Alignment]
  * [http://bioruby.open-bio.org/rdoc/classes/Bio/Sequence.html Bio::Sequence]
 
+=== Creating a Multiple Sequence Alignment ===
+
+
+=== Creating a Multiple Sequence Alignment from a Database ===
+
+?
+
 === Writing a Multiple Sequence Alignment to a File ===