[BioRuby-cvs] bioruby/doc Tutorial.rd,1.14,1.15
Pjotr Prins
pjotr at dev.open-bio.org
Sat Feb 2 14:02:03 UTC 2008
Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31273
Modified Files:
Tutorial.rd
Log Message:
Updating tutorial
Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Tutorial.rd 2 Feb 2008 13:03:23 -0000 1.14
--- Tutorial.rd 2 Feb 2008 14:01:54 -0000 1.15
***************
*** 3,7 ****
# 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!
--- 3,12 ----
# A possible test run could be from rdtool:
#
! # ruby -I lib ./bin/rd2 ~/cvs/opensource/bioruby/doc/Tutorial.rd
! #
! # or with style sheet:
! #
! # ruby -I lib ./bin/rd2 -r rd/rd2html-lib.rb --with-c
! ss=bioruby.css ~/cvs/opensource/bioruby/doc/Tutorial.rd > ~/bioruby.html
#
# A common problem is tabs in the text file!
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*** 9,39 ****
=begin
! See the document in the CVS repository ./doc/((<Tutorial.rd|URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain>)) - for a potentially more up-to-date edition. This one was updated:
!
! $Id$
! 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
! repository. Please edit the file there otherwise changes may get
! lost. See ((<BioRuby Developer Information>)) for CVS and mailing list
! access.
! = BioRuby Tutorial
== Introduction
! This is a tutorial for using Bioruby. For BioRuby you need to install
! Ruby and the BioRuby package on your computer. For each following the
! instruction on the respective websites. (EDITOR's NOTE: include URL's)
!
! (EDITOR's NOTE: describe rdoc use for individual classes)
! For further information on the Ruby language see the section 'Further
! reading' at the end.
You can check whether Ruby is installed on your computer and what
--- 14,40 ----
=begin
! = BioRuby Tutorial
! Editor: PjotrPrins <p .at. bioruby.org>
! * Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>
! * Copyright (C) 2005-2008 Pjotr Prins, Naohisa Goto and others
! The latest version resides in the CVS repository ./doc/((<Tutorial.rd|URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain>)). This one was updated:
! $Id$
! in preparation for the ((<BioHackathlon 2008|URL:http://hackathon.dbcls.jp/>))
== Introduction
! This is a tutorial for using Bioruby. A basic knowledge of Ruby is required.
! If you want to know more about the programming langauge Ruby we recommend the
! excellent book ((<Programming Ruby|URL:http://www.pragprog.com/titles/ruby>))
! by Dave Thomas and Andy Hunt - some of it is online
! ((<here|URL:http://www.rubycentral.com/pickaxe/>)).
! For BioRuby you need to install
! Ruby and the BioRuby package on your computer.
You can check whether Ruby is installed on your computer and what
***************
*** 46,49 ****
--- 47,61 ----
ruby 1.8.5 (2006-08-25) [powerpc-linux]
+ If you see no such thing you'll have to install Ruby using your installation
+ manager. For more information see the
+ ((<Ruby|URL:http://www.ruby-lang.org/en/>)) website.
+
+ Once Ruby is works download and install Bioruby using the links on the
+ ((<Bioruby|URL:http://bioruby.org/>)) website.
+
+ A lot of BioRuby's documentation exists in the source code and unit tests. To
+ really dive in you will need the latest source code tree. The embedded rdoc
+ documentation can be viewed online at
+ ((<bioruby's rdoc|URL:http://bioruby.org/rdoc/>)). But first lets start!
== Trying Bioruby
***************
*** 52,56 ****
following command
! $BIORUBY/bin/bioruby
and you should see a prompt
--- 64,68 ----
following command
! ./bin/bioruby
and you should see a prompt
***************
*** 93,97 ****
puts seq.translate # translation (Bio::Sequence::AA object)
puts seq.translate(2) # translation from frame 2 (default is frame 1)
! puts seq.translate(1,11) # using codon table No.11 (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
p seq.translate.codes # shows three-letter codes (Array)
--- 105,110 ----
puts seq.translate # translation (Bio::Sequence::AA object)
puts seq.translate(2) # translation from frame 2 (default is frame 1)
! puts seq.translate(1,11) # using codon table No.11
! # (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
p seq.translate.codes # shows three-letter codes (Array)
***************
*** 114,120 ****
% ri File.open
! Nucleic acid sequence is an object of +Bio::Sequence::NA+ class, and
! amino acid sequence is an object of +Bio::Sequence::AA+ class. Shared
! methods are in the parent +Bio::Sequence+ class.
As Bio::Sequence class inherits Ruby's String class, you can use
--- 127,133 ----
% ri File.open
! Nucleic acid sequence is an object of Bio::Sequence::NA class, and
! amino acid sequence is an object of Bio::Sequence::AA class. Shared
! methods are in the parent Bio::Sequence class.
As Bio::Sequence class inherits Ruby's String class, you can use
***************
*** 297,303 ****
end
- (TRANSLATOR'S NOTE: Bio::DB.open have not been used so well.)
- (EDITOR's NOTE: Test code)
-
Next, we are going to parse the GenBank 'features', which is normally
very complicated:
--- 310,313 ----
***************
*** 382,387 ****
Databases in BioRuby are essentially accessed like that of GenBank
! with classes like Bio::GenBank, Bio::KEGG::GENES,
! (EDITOR's NOTE: include complete list)
In many cases the Bio::DatabaseClass acts as a factory pattern
--- 392,397 ----
Databases in BioRuby are essentially accessed like that of GenBank
! with classes like Bio::GenBank, Bio::KEGG::GENES. A full list can be found in
! the ./lib/bio/db directory of the BioRuby source tree.
In many cases the Bio::DatabaseClass acts as a factory pattern
***************
*** 1151,1160 ****
== Further reading
! See the BioRuby in anger Wiki and the class documentation for more
! information on BioRuby.
- The best book to get for understanding and getting productive with the
- Ruby language is 'Programming Ruby' by Dave Thomas and Andy
- Hunt. Strongly recommended!
= APPENDIX
--- 1161,1169 ----
== Further reading
! See the BioRuby in anger Wiki. A lot of BioRuby's documentation exists in the
! source code and unit tests. To really dive in you will need the latest source
! code tree. The embedded rdoc documentation can be viewed online at
! ((<URL:http://bioruby.org/rdoc/>)).
= APPENDIX
***************
*** 1189,1191 ****
--- 1198,1207 ----
carefully that come with each package.
+ == Modifying this page
+
+ IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
+ repository. Please edit the file there otherwise changes may get
+ lost. See ((<BioRuby Developer Information>)) for CVS and mailing list
+ access.
+
=end
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