From 6639ef7ab715a18637ce7300707fa48bf77c0de6 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 17:31:36 +0000 Subject: [PATCH] in progress... --- forester/ruby/scripts/bioruby_examples/msa_1.rb | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/forester/ruby/scripts/bioruby_examples/msa_1.rb b/forester/ruby/scripts/bioruby_examples/msa_1.rb index dca6106..9c977e5 100644 --- a/forester/ruby/scripts/bioruby_examples/msa_1.rb +++ b/forester/ruby/scripts/bioruby_examples/msa_1.rb @@ -15,20 +15,25 @@ require 'bio' -seq1 = "KMLFGVVFFFGG" -seq2 ="LMGGHHF" -seq3 = "GKKKKGHHHGHRRRGR" -seq4 = "KKKGHHHGHRERGR" -seqs = [ seq1, seq2, seq3, seq4 ] +seqs = [ "KMLFGVVFFFGG", + "LMGGHHF", + "GKKKKGHHHGHRRRGR", + "KKKKGHHHGHRRRGR" ] # MAFFT options = [ '--maxiterate', '1000', '--localpair' ] mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options ) report = mafft.query_align( seqs) -#puts report.alignment.output_fasta -report.alignment.each { |x| puts x.to_s } -puts 'OK' + +# Accesses the actual alignment +align = report.alignment + +# Prints each sequence to the console. +align.each { |s| puts s.to_s } + + +puts 'MAFFT OK' puts #clustalw -- 1.7.10.2