[BioRuby-cvs] bioruby/doc Tutorial.rd,1.12,1.13

[Pjotr Prins]

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv30404/doc

Modified Files:
	Tutorial.rd 
Log Message:
Updated tutorial to include generating a random sequence and an example
of using the rebase library.



Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** Tutorial.rd	17 Feb 2006 14:59:26 -0000	1.12
--- Tutorial.rd	9 Jul 2007 12:28:07 -0000	1.13
***************
*** 9,16 ****
  Editor:                  PjotrPrins <p at bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k at bioruby.org>, 2005-2006 all
! others
! 
! NOTE: This page is a work in progress at this point
  
  IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
--- 9,13 ----
  Editor:                  PjotrPrins <p at bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k at bioruby.org>, 2005-2007 Pjotr Prins, Naohisa Goto and others
  
  IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
***************
*** 39,43 ****
  command. Showing something like:
  
!   ruby 1.8.2 (2005-04-11) [powerpc-linux]
  
  
--- 36,40 ----
  command. Showing something like:
  
!   ruby 1.8.5 (2006-08-25) [powerpc-linux]
  
  
***************
*** 97,100 ****
--- 94,100 ----
      puts seq.complement.translate       # translation of complemental strand
  
+ 		counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
+     p randomseq = Bio::Sequence::NA.randomize(counts)  # reshuffle sequence with same freq.
+ 
  The p, print and puts methods are standard Ruby ways of outputting to
  the screen. If you want to know more about standard Ruby commands you
***************
*** 463,466 ****
--- 463,500 ----
    a2 = a.do_align(factory)
  
+ == Restriction Enzymes (Bio::RE)
+ 
+ BioRuby has extensive support for restriction enzymes (REs). It contains a full
+ library of commonly used REs (from REBASE) which can be used to cut single
+ stranded RNA or dubbel stranded DNA into fragments. To list all enzymes:
+ 
+   rebase = Bio::RestrictionEnzyme.rebase
+ 	rebase.each do |enzyme_name, info|
+ 		p enzyme_name
+   end
+ 
+ and cut a sequence with an enzyme follow up with:
+ 
+    res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0}, {:view_ranges => true})
+    if res.kind_of? Symbol #error
+       err = Err.find_by_code(res.to_s)
+       unless err
+         err = Err.new(:code => res.to_s)
+       end
+    end
+ 	 res.each do |frag|
+ 	    em = EnzymeMatch.new
+ 
+       em.p_left = frag.p_left
+       em.p_right = frag.p_right
+       em.c_left = frag.c_left
+       em.c_right = frag.c_right
+ 
+       em.err = nil
+       em.enzyme = ar_enz
+       em.sequence = ar_seq
+ 			p em
+     end
+ 
  
  == Sequence homology search by using the FASTA program (Bio::Fasta)
***************
*** 1124,1135 ****
    * ((<URL:http://www.genome.jp/kegg/soap/>))
  
  == Using BioRuby with R
  
! The R libraries can be accessed from Ruby using the @@FIXME
! package. This allows at least use of the standard R library
! functions. Unfortunately there is no binding for dynamic R - so at
! this point you'll have to create some command line interface.
  
! == Using BioPerl from Ruby
  
  == Installing required external library
--- 1158,1172 ----
    * ((<URL:http://www.genome.jp/kegg/soap/>))
  
+ == Comparing BioProjects
+ 
+ For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see ((<http://sciruby.codeforpeople.com/sr.cgi/BioProjects>))
+ 
  == Using BioRuby with R
  
! Using Ruby with R Pjotr wrote a section on SciRuby. See ((<ULR:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang>))
  
! == Using BioPerl or BioPython from Ruby
! 
! At the moment there is no easy way of accessing BioPerl from Ruby. The best way, perhaps, is to create a Perl server that gets accessed through XML/RPC or SOAP.
  
  == Installing required external library