[BioRuby-cvs] bioruby/doc Tutorial.rd,1.13,1.14

[Pjotr Prins]

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31174

Modified Files:
	Tutorial.rd 
Log Message:
Tabs in the Tutorial broke the rd parser - the Wiki will be fixed now.



Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Tutorial.rd	9 Jul 2007 12:28:07 -0000	1.13
--- Tutorial.rd	2 Feb 2008 13:03:23 -0000	1.14
***************
*** 1,2 ****
--- 1,10 ----
+ # This document is generated with a version of rd2html (part of Hiki)
+ #
+ # A possible test run could be from rdtool:
+ #
+ #   ruby -I lib ./bin/rd2 ~/izip/cvs/opensource/bioruby/doc/Tutorial.rd
+ #
+ # A common problem is tabs in the text file!
+ 
  =begin
  
***************
*** 5,13 ****
    $Id$
  
! Translated into English: Naohisa Goto <ng at bioruby.org>
  
! 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
--- 13,21 ----
    $Id$
  
! Translated into English: Naohisa Goto <ng .at. bioruby.org>
  
! Editor:                  PjotrPrins <p .at. bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>, 2005-2008 Pjotr Prins, Naohisa Goto and others
  
  IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
***************
*** 32,36 ****
  version it has with the
  
! 	% ruby -v
  
  command. Showing something like:
--- 40,44 ----
  version it has with the
  
!   % ruby -v
  
  command. Showing something like:
***************
*** 55,59 ****
    bioruby> puts seq
    atgcatgcaaaa
!   bioruby> puts seq.complement 
    ttttgcatgcat
  
--- 63,67 ----
    bioruby> puts seq
    atgcatgcaaaa
!   bioruby> puts seq.complement
    ttttgcatgcat
  
***************
*** 94,98 ****
      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.
  
--- 102,106 ----
      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.
  
***************
*** 159,163 ****
  * Divide a genome sequence into sections of 10000bp and
    output FASTA formatted sequences. The 1000bp at the start and end of
! 	each subsequence overlapped. At the 3' end of the sequence the
    leftover subsequence shorter than 10000bp is also added
  
--- 167,171 ----
  * Divide a genome sequence into sections of 10000bp and
    output FASTA formatted sequences. The 1000bp at the start and end of
!   each subsequence overlapped. At the 3' end of the sequence the
    leftover subsequence shorter than 10000bp is also added
  
***************
*** 252,258 ****
  
      #!/usr/bin/env ruby
!   
      require 'bio'
!     
      ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
      ff.each_entry do |gb|
--- 260,266 ----
  
      #!/usr/bin/env ruby
! 
      require 'bio'
! 
      ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
      ff.each_entry do |gb|
***************
*** 470,475 ****
  
    rebase = Bio::RestrictionEnzyme.rebase
! 	rebase.each do |enzyme_name, info|
! 		p enzyme_name
    end
  
--- 478,483 ----
  
    rebase = Bio::RestrictionEnzyme.rebase
!   rebase.each do |enzyme_name, info|
!     p enzyme_name
    end
  
***************
*** 483,488 ****
        end
     end
! 	 res.each do |frag|
! 	    em = EnzymeMatch.new
  
        em.p_left = frag.p_left
--- 491,496 ----
        end
     end
!    res.each do |frag|
!       em = EnzymeMatch.new
  
        em.p_left = frag.p_left
***************
*** 494,498 ****
        em.enzyme = ar_enz
        em.sequence = ar_seq
! 			p em
      end
  
--- 502,506 ----
        em.enzyme = ar_enz
        em.sequence = ar_seq
!       p em
      end
  
***************
*** 1160,1168 ****
  == 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
--- 1168,1176 ----
  == Comparing BioProjects
  
! For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see ((<URL:http://sciruby.codeforpeople.com/sr.cgi/BioProjects>))
  
  == Using BioRuby with R
  
! Using Ruby with R Pjotr wrote a section on SciRuby. See ((<URL:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang>))
  
  == Using BioPerl or BioPython from Ruby
***************
*** 1182,1184 ****
  
  =end
- 
--- 1190,1191 ----