[BioRuby-cvs] bioruby/doc Tutorial.rd,1.11,1.12

[Pjotr Prins]

Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv30194/doc

Modified Files:
	Tutorial.rd 
Log Message:
Fixed tutorial on updated sequence handling (throw exception instead of 
return nil value)

Added a FASTA output example that allows for regex filtering like
  any2fasta.rb "/GAT[CT]/i" *.seq > reduced.fasta



Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Tutorial.rd	31 Jan 2006 07:45:22 -0000	1.11
--- Tutorial.rd	17 Feb 2006 14:59:26 -0000	1.12
***************
*** 7,11 ****
  Translated into English: Naohisa Goto <ng at bioruby.org>
  
! Editor:                  PjotrPrins
  
  Copyright (C) 2001-2003 KATAYAMA Toshiaki <k at bioruby.org>, 2005-2006 all
--- 7,11 ----
  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>, 2005-2006 all
***************
*** 128,136 ****
  
  So when using String methods, you should subtract 1 from positions
! conventionally used in biology.  (subseq method returns nil if you
! specify positions smaller than or equal to 0 for either one of the
! "from" or "to".)
! 
! (EDITOR'S NOTE: should 'subseq' not throw an exception instead?)
  
  The window_search(window_size, step_size) method shows a typical Ruby
--- 128,134 ----
  
  So when using String methods, you should subtract 1 from positions
! conventionally used in biology.  (subseq method will throw an exception if you
! specify positions smaller than or equal to 0 for either one of the "from" or
! "to".)
  
  The window_search(window_size, step_size) method shows a typical Ruby
***************
*** 402,405 ****
--- 400,406 ----
        p entry.seq               # sequence data of the entry
      end
+ 
+ An example that can take any input, filter using a regular expression to output
+ to a FASTA file can be found in sample/any2fasta.rb.
  
  Other methods to extract specific data from database objects can be