X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FPhyloBioRuby.wiki;h=75b98ecd9ea92e6f066f2ad04ebca52dacab0707;hb=d08eccd316f7c95738f7f7e708f99a4398c63d7d;hp=a3be9609e4686c7e01d25b590957af1e70c44b88;hpb=3b13b835acf5bc4ed44cf28682a846e748f9b46b;p=jalview.git diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index a3be960..75b98ec 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. @@ -91,6 +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 ===