X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=4b6b45ffa63c3c20de0a76453f618aa7b8714b94;hb=51067a27d785cb31fbd3d8fd81b09b0d140efdff;hp=ab6faf9d1c6fc050e9b264ed01fd4959810a9161;hpb=0a133c612b5c1acc1436a94b0d65af27dd4bba42;p=jalview.git

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index ab6faf9..4b6b45f 100644
--- 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 +23,41 @@ 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.
 
 {{{
@@ -43,28 +78,32 @@ msa.each do |entry|
 end
 }}}
 
-Blah
+==== FASTA Format ====
+
+The following example shows how to read in a *FASTA*-formatted multiple sequence file. (_This seems a little clumsy, I wonder if there is a more direct way, avoiding the creation of an array.)
 {{{
-# 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.
-File.open('out1.phylip', 'w') do |f|
+# to a file in PHYLIP format.
+File.open('outfile.phylip', 'w') do |f|
   f.write(seqs.output(:phylip))
 end
 }}}
@@ -75,6 +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 ===