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.
=== 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.
{{{
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
}}}
* [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 ===