From 38da32cb0c33e259d49e3515e19922655f32a26b Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 1 Mar 2011 03:02:40 +0000 Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface. --- wiki/PhyloBioRuby.wiki | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki index f87b96c..0cd5930 100644 --- a/wiki/PhyloBioRuby.wiki +++ b/wiki/PhyloBioRuby.wiki @@ -23,7 +23,7 @@ Copyright (C) 2011 Christian M Zmasek === Reading in a Multiple Sequence Alignment from a File === -Reading in a ClustalW-formatted multiple sequence alignment: +The follow example shows how to read in a *ClustalW*-formatted multiple sequence alignment. {{{ #!/usr/bin/env ruby @@ -47,7 +47,8 @@ end === Writing a Multiple Sequence Alignment to a File === -Writing a multiple sequence alignment in fasta format: + +The follow example shows how to writing a multiple sequence alignment in *Fasta*-format: {{{ #!/usr/bin/env ruby @@ -60,19 +61,19 @@ File.open('outfile.fasta', 'w') do |f| end }}} +The following constants a -Writing a multiple sequence alignment in clustalw format: +* ClustalW: :clustal +* Fasta: :fasta +* Phylip interleaved: :phylip +* Phylip non-interleaved: :phylipnon +* MSF: :msf +* Molphy: :molphy -{{{ -#!/usr/bin/env ruby -require 'bio' -# Creates a new file named "outfile.aln" and writes -# multiple sequence alignment 'align' to it in clustal format. -File.open('outfile.aln', 'w') do |f| - f.write(align.output(:clustal)) -end -}}} +For example, the following writes in Phylip's non-interleaved format: + +`f.write(align.output(:phylipnon))` == Calculating Multiple Sequence Alignments == -- 1.7.10.2