Commit 6ef6e6ce authored by Lucas Nussbaum's avatar Lucas Nussbaum

Imported Upstream version 1.4.1

parents
BioRuby is copyrighted free software by Toshiaki Katayama <k@bioruby.org>.
You can redistribute it and/or modify it under either the terms of the GPL
version 2 (see the file GPL), or the conditions below:
1. You may make and give away verbatim copies of the source form of the
software without restriction, provided that you duplicate all of the
original copyright notices and associated disclaimers.
2. You may modify your copy of the software in any way, provided that
you do at least ONE of the following:
a) place your modifications in the Public Domain or otherwise
make them Freely Available, such as by posting said
modifications to Usenet or an equivalent medium, or by allowing
the author to include your modifications in the software.
b) use the modified software only within your corporation or
organization.
c) give non-standard binaries non-standard names, with
instructions on where to get the original software distribution.
d) make other distribution arrangements with the author.
3. You may distribute the software in object code or binary form,
provided that you do at least ONE of the following:
a) distribute the binaries and library files of the software,
together with instructions (in the manual page or equivalent)
on where to get the original distribution.
b) accompany the distribution with the machine-readable source of
the software.
c) give non-standard binaries non-standard names, with
instructions on where to get the original software distribution.
d) make other distribution arrangements with the author.
4. You may modify and include the part of the software into any other
software (possibly commercial). But some files in the distribution
are not written by the author, so that they are not under these terms.
For the list of those files and their copying conditions, see the
file LEGAL.
5. The scripts and library files supplied as input to or produced as
output from the software do not automatically fall under the
copyright of the software, but belong to whomever generated them,
and may be sold commercially, and may be aggregated with this
software.
6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE.
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= KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
Copyright:: Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
License:: The Ruby License
= Known issues and bugs in BioRuby
Below are known issues and bugs in BioRuby. Patches to fix them are welcome.
We hope they will be fixed in the future.
Items marked with (WONT_FIX) tags would not be fixed within BioRuby because
they are not BioRuby's issues and/or it is very difficult to fix them.
== 1. Ruby version specific issues
=== Ruby 1.9.1 or later
Some classes/modules/methods still may not work or may return incorrect
results in Ruby 1.9.1, especially those not covered by the unit tests.
==== String encodings
Currently, BioRuby do not care string encodings. In some cases,
Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
(encoding name)" may be raised.
=== Ruby 1.9.0
(WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
Use Ruby 1.9.1 or later.
=== Ruby 1.8.2 or earlier
(WONT_FIX) In some cases, temporary files and directories may not be
removed because of the lack of FileUtils.remove_entry_secure.
(WONT_FIX) We will soon end support for Ruby 1.8.2. Note that Ruby
1.8.1 or earlier is no longer supported, as described in README.rdoc.
=== Issues about SOAP/WSDL
SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
In addition, because of the API changes in recent SOAP4R, some
classes/modules using SOAP4R may not work.
=== Problem with REXML DoS vulnerability patch before 09-Nov-2008
(WONT_FIX) If you have applied a patch taken from
http://www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/
before 09 Nov 2008 12:40 +0900, because of the bug in the patch,
parsing of Blast XML results with REXML parser may fail. The bug is already
fixed and new patch is available on the above URL. Note that some Linux
distributions would have incorporated the patch in their manners, and may
have the same problem.
== 2. OS and/or architecture-dependent issues
=== Microsoft Windows
==== Text mode issues
Following 4 tests failed on mswin32 (and maybe on mingw32 and bccwin32)
because of the conversion of line feed codes in the text mode.
* test_ended_pos and test_start_pos in test/unit/bio/io/test_flatfile.rb
* test_pos in test/unit/bio/io/flatfile/test_buffer.rb
* test_entry_pos in test/unit/bio/appl/blast/test_rpsblast.rb
This indicates that br_bioflat.rb and Bio::FlatFileIndex may create
incorrect indexes on mswin32, mingw32, and bccwin32. In addition,
Bio::FlatFile may return incorrect data.
==== String escaping of command-line arguments
After BioRuby 1.4.1, in Ruby 1.9.X running on Windows, escaping of
command-line arguments are processed by the Ruby interpreter. Before BioRuby
1.4.0, the escaping is executed in Bio::Command#escape_shell_windows, and
the behavior is different from the Ruby interpreter's one.
Curreltly, due to the change, test/functional/bio/test_command.rb may fail
on Windows with Ruby 1.9.X.
==== Windows 95/98/98SE/ME
(WONT_FIX) Some methods that call external programs may not work in
Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
=== OpenVMS, BeOS, OS/2, djgpp, Windows CE
(WONT_FIX) BioRuby may not work on these platforms.
== 3. Known issues and bugs in BioRuby
=== Bio::Ensembl
Due to the renewal of Ensembl web site, Bio::Ensembl does not work for
the latest Ensembl. For a workaround, use an archive server. For example,
"jul2008.archive.ensembl.org" seems to be the last server before the renewal.
human = Bio::Ensembl.new("Homo_sapiens", "jul2008.archive.ensembl.org")
Alternatively, consider using Ruby Ensembl API.
* http://github.com/jandot/ruby-ensembl-api
=== Bio::DBGET and sample/dbget
(WONT_FIX) Because the DBGET service have not been publically available for
a long time, we give up support for Bio::DBGET and sample/dbget. Instead,
using Bio::TogoWS or Bio::KEGG::API is recommended.
=== Bio::NCBI::SOAP
It seems that Bio::NCBI::SOAP (in lib/bio/io/ncbisoap.rb) does not work
correctly, even running on Ruby 1.8.x. Instead, use Bio::NCBI::REST.
=== Bio::KEGG::Taxonomy and sample/demo_kegg_taxonomy.rb
Bio::KEGG::Taxonomy fails to parse current KEGG taxonomy data file probably
because of the growth of the data size.
== 4. Compatibility issues with other libraries/extensions
=== ActiveRecord
BioSQL support uses ActiveRecord, but the author of the document does not
know which version is suitable.
=== Ruby on Rails
BioRuby Shell on Web uses Ruby on Rails, but the author of the document does
not know which version is suitable.
LEGAL NOTICE INFORMATION
------------------------
All the files in this distribution are covered under either the Ruby's
license (see the file COPYING) or public-domain except some files
mentioned below.
setup.rb:
Copyright (c) 2000-2006 Minero Aoki
This program is free software.
You can distribute/modify this program under the terms of
the GNU LGPL, Lesser General Public License version 2.1.
sample/any2fasta.rb:
Copyright (C) 2006 Pjotr Prins <p@bioruby.org>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
sample/biofetch.rb:
Copyright (C) 2002-2004 KATAYAMA Toshiaki <k@bioruby.org>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
sample/enzymes.rb:
Copyright (C) 2006 Pjotr Prins <p@bioruby.org> and
Trevor Wennblom <trevor@corevx.com>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
sample/fasta2tab.rb:
sample/fsplit.rb:
sample/gb2tab.rb:
sample/genes2nuc.rb:
sample/genes2pep.rb:
sample/genes2tab.rb:
sample/genome2tab.rb:
sample/gt2fasta.rb:
sample/ssearch2tab.rb:
sample/tfastx2tab.rb:
sample/vs-genes.rb:
Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
sample/fastagrep.rb:
sample/fastasort.rb:
sample/na2aa.rb:
Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
sample/gb2fasta.rb:
Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
Copyright (C) 2002 Yoshinori K. Okuji <o@bioruby.org>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
sample/gbtab2mysql.rb:
sample/genome2rb.rb:
sample/pmfetch.rb:
sample/pmsearch.rb:
Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
sample/tdiary.rb:
Copyright (C) 2003 KATAYAMA Toshiaki <k@bioruby.org>
Mitsuteru C. Nakao <n@bioruby.org>
Itoshi NIKAIDO <itoshi@gsc.riken.go.jp>
Takeya KASUKAWA <kasukawa@gsc.riken.go.jp>
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
test/data/uniprot/p53_human.uniprot:
This Swiss-Prot entry is copyright. It is produced through a collaboration
between the Swiss Institute of Bioinformatics and the EMBL outstation -
the European Bioinformatics Institute. There are no restrictions on its
use as long as its content is in no way modified and this statement is not
removed.
GPL:
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
LGPL:
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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--
= README.rdoc - README for BioRuby
Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>,
Copyright (C) 2008 Jan Aerts <jandot@bioruby.org>
License:: The Ruby License
* The above statement is limited to this file. See below about BioRuby's
copyright and license.
++
= BioRuby
Copyright (C) 2001-2010 Toshiaki Katayama <k@bioruby.org>
BioRuby is an open source Ruby library for developing bioinformatics
software. Object oriented scripting language Ruby has many features
suitable for bioinformatics research, for example, clear syntax to
express complex objects, regular expressions for text handling as
powerful as Perl's, a wide variety of libraries including web service
etc. As the syntax of the Ruby language is simple and very clean, we
believe that it is easy to learn for beginners, easy to use for
biologists, and also powerful enough for the software developers.
In BioRuby, you can retrieve biological database entries from flat
files, internet web servers and local relational databases. These
database entries can be parsed to extract information you need.
Biological sequences can be treated with the fulfilling methods of the
Ruby's String class and with regular expressions. Daily tools like
Blast, Fasta, Hmmer and many other software packages for biological
analysis can be executed within the BioRuby script, and the results
can be fully parsed to extract the portion you need. BioRuby supports
major biological database formats and provides many ways for accessing
them through flatfile indexing, SQL, web services etc. Various web
services including KEGG API can be easily utilized by BioRuby.
== FOR MORE INFORMATION
=== Documents in this distribution
==== General information
README.rdoc:: This file. General information and installation procedure.
RELEASE_NOTES.rdoc:: News and important changes in this release.
KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
==== Tutorials and other useful information
doc/Tutorial.rd:: BioRuby Tutorial.
doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
==== BioRuby development
ChangeLog:: History of changes.
README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
==== Documents written in Japanese
doc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.
doc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.
doc/KEGG_API.rd.ja:: Japanese translation of KEGG_API.rd.
=== WWW
BioRuby's official website is at http://bioruby.org/.
You will find links to related resources including downloads,
mailing lists, Wiki documentation etc. in the top page.
* http://bioruby.org/
== WHERE TO OBTAIN
=== WWW
The stable release is freely available from the BioRuby website.
* http://bioruby.org/archive/
=== RubyGems
RubyGems[URL:http://rubyforge.org/projects/rubygems/] version of
the BioRuby package is also available for easy installation.
* http://rubyforge.org/projects/bioruby/
=== git
If you need the latest development version, this is provided at
* http://github.com/bioruby/bioruby
and can be obtained by the following procedure:
% git clone git://github.com/bioruby/bioruby.git
==== CVS
CVS is now deprecated as source control has moved to github. Please use git
instead of CVS. For historical purposes: the anonymous CVS was provided at
* http://cvs.bioruby.org/
and could be obtained by the following procedure.
% cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login