bio 1.0.0 → 1.1.0

data/doc/TODO.rd.ja

@@ -1,138 +0,0 @@
-=begin
-
-  $Id: TODO.rd.ja,v 1.16 2004/08/24 00:18:03 k Exp $
-
-  Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
-
-= TODO
-
-* �����꡼��
-
-* �ɥ�����ȹ���
-  * ���塼�ȥꥢ���ɵ�
-  * �Ѹ첽
-  * RDoc
-
-* ����ץ����� (*2tab �Ȥ�)
-  * sample/README.rd[.ja]
-
-* cvs.open-bio.org �Υɥ�����ȹ���
-
-* Bio::SQL update, name space
-
-* Bio::Fetch
-  * E-Utils
-  * http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
-
-
-* Bio::Location location coordinate system (style)
-
-* GenBank, EMBL, SPTR, BioSQL �����硢�ե����ޥå�����Ѵ�
-  * genbank/ @moltype
-  * bio/db/seqentry.rb �� bio/seqentry.rb ������˥���ƥ� SeqEntry ����
-    * InternalSeq �Ȥ��Ǥ⡩
-  * lib/bio/db/genbank/, embl/ ��ե��������
-    * Bio::SQL::Sequence ��ޤ᤿������¤
-    * genpept, refseq(NP_)
-    * Bio::Reference ���饹 �� EMBL �ˤ�?
-  * test GenBank >350k
-
-* Blast, Fasta, Hmmer
-  * blast, hmmer �Υ�ݡ��� -> Bio::FlatFile ����⥢������
-  * bio/appl/fasta/report.rb, bio/appl/hmmer/report.rb ����ƥʳ��Ф�
-  * lib/bio/appl/blast/xmlparser.rb  " problem
-  * lib/bio/appl/megablast.rb �ɲá�
-  * Blast HSP tiling [bioperl-l 2002 8/13,4,5 ?]
-    * Bio::Blast::Report::Hit#total_alignment_length
-    * Bio::Blast::Report::Hit#total_identical_residues
-    * Bio::Blast::Report::Hit#total_convserved_residues
-
-* MAFFT, T-Coffee, CLUSTALW �� ���饤�����
-  * ���饤���ȥ��֥�������
-    * class Bio::Alignment ?
-    * class Bio::Alignment::Pairwise or class Bio::PairwiseAlignment ?
-    * class Bio::Alignment::Multiple or class Bio::MultipleAlignment ?
-    * ���饤���ȥӥ塼����ۤ���
-  * Blast refactering
-  * AlignFactory -> SearchIO��
-  * Bio::Align �� Bio::Blast::Report �ʤɤΥ��饤���Ȥ�
-    �ݻ�����ΤˤĤ���
-  * ���饤����ȥ��饹�� CIGAR �ե����ޥå�
-
-* KGML�ѡ���
-  * Pathway���饹��dijkstra -> Graph
-  * Tree���饹
-
-* lib/bio/db/kegg/keggtab.rb �� lib/bio/data/keggorg.rb �����硩
-
-* Bio::LSID [bioperl-l 2002 7/15 seq namespace method]
-
-* �����ǥ��󥰥�������
-  * camelCase �ػ�
-  * = �κ����϶�����
-  * tab �ʤ� 2 ���ڡ�������ǥ��
-  * �ǽ�Ū�ˤ� RDoc �ղá� (Rimport ��Ȥ��Τ���������)
-  * ���饹̾���⥸�塼��̾�� camelCase���������ʸ���� _ �Ƕ��ڤ�
-  * Array, Hash�ʾ�˥ͥ��Ȥ����饯�饹��������
-
-=== DB
-
-* ����ȥ����� (GO etc.) ������
-
-* ������շ� InterPro (incl. Pfam etc.) ������
-
-* SSDB
-
-* COG
-
-* PDB or PDBj �ѡ���
-  * challange CASP? :)
-
-=== ����
-
-* Ruby 1.8
-  * stringIO
-  * autoload
-  * Array.new(num) { Hoge.new }
-
-* ext/
-  * �������٤��᥽�å� C �� ?
-
-* ����֤�ѥ��벽���뤿��Υ��饹
-
-* �ƥ��ȴĶ�������
-  * Test::Unit �Ȥ���
-    * �����ե����롢�ͥåȥ����������ɤ����뤫
-  * ���󥹥ȡ������ make check �ߤ����ʤ��Ȥ򤹤뤫
-
-* ����å�
-  * ���ΤȤ������ޤ�Ȥ����̤Ϥʤ������Τ�ʤ����ɡ� GUI �Ȥ��ǡ�
-
-* �ɥ����������
-  * Thai
-  * Korea
-  * Russia
-  * French
-
-== OTHERS
-
-* midi
-
-* q--p
-  * RSS
-  * tDiary
-
-* gb.bioruby.org �� GFF, DAS �б�
-  * �ݥ������������ץ�ʥ��ޥ�ɥ饤��/CGI��
-  * Ming��
-
-* R, SVM/RVM, ����� ��
-
-* Ruby/Cocoa, Ruby/Gtk �ˤ�� GUI �ʥե����ȥ꡼
-  * gsequence
-  * biograph
-  * GO �� xml �� GtkTree �� ����­��̡�
-
-* ��
-
-=end

data/lib/bio/appl/fasta/format6.rb

@@ -1,37 +0,0 @@
-#
-# bio/appl/fasta/format6.rb - FASTA output (-m 6) parser
-# 
-#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
-#
-#  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.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: format6.rb,v 1.2 2005/09/08 01:22:09 k Exp $
-#
-
-module Bio
-  class Fasta
-
-    class Report
-
-      # will be ported from sample/{fasta2tab,ssearch2tab,tfastx2tab}.rb
-
-      def initialize
-        raise NotImplementedError
-      end
-    end
-
-  end
-end
-

data/lib/bio/db/kegg/cell.rb

@@ -1,88 +0,0 @@
-#
-# bio/db/kegg/cell.rb - KEGG/CELL database class
-#
-#   Copyright (C) 2001 KAWASHIMA Shuichi <s@bioruby.org>
-#
-#  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.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: cell.rb,v 1.7 2005/09/08 01:22:11 k Exp $
-#
-
-require "bio/db"
-
-module Bio
-
-  class KEGG
-
-    class CELL < KEGGDB
-
-      DELIMITER	= RS = "\n///\n"
-      TAGSIZE	= 12
-
-      def initialize(entry)
-        super(entry, TAGSIZE)
-      end
-
-      def entry_id
-        field_fetch('ENTRY')
-      end
-
-      def definition
-        field_fetch('DEFINITION')
-      end
-
-      def org
-        field_fetch('ORGANISM')
-      end
-      alias organism org
-
-      def mother
-        field_fetch('MOTHER')
-      end
-
-      def daughter
-        field_fetch('DAUGHTER').gsub(/ /, '').split(/,/)
-      end
-
-      def sister
-        field_fetch('SISTER')
-      end
-
-      def fate
-        field_fetch('CELL_FATE').gsub(/ /, '').split(/,/)
-      end
-
-      def contact
-        field_fetch('CONTACT').gsub(/ /, '').split(/,/)
-      end
-
-      def expression
-        field_fetch('EXPRESSION')
-      end
-
-      def fig
-        field_fetch('FIGURE')
-      end
-
-      def ref
-        field_fetch('REFERENCE')
-      end
-
-    end
-
-  end
-
-end
-

data/lib/bio/db/kegg/ko.rb

@@ -1,178 +0,0 @@
-#
-# bio/db/kegg/ko.rb - KO (KEGG Orthology) database class
-#
-#   Copyright (C) 2003 KATAYAMA Toshiaki <k@bioruby.org>
-#   Copyright (C) 2003 Masumi Itoh <m@bioruby.org>
-#
-#  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.
-#
-#  This library is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#  Lesser General Public License for more details.
-#
-#  You should have received a copy of the GNU Lesser General Public
-#  License along with this library; if not, write to the Free Software
-#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
-#
-#  $Id: ko.rb,v 1.5 2005/09/08 01:22:11 k Exp $
-#
-
-require 'bio/db'
-
-module Bio
-
-  class KEGG
-    
-    class KO < KEGGDB
-      
-      DELIMITER	= RS = "\n///\n"
-      TAGSIZE	= 12
-
-      def initialize(entry)
-        super(entry, TAGSIZE)
-      end
-      
-      
-      def entry_id
-        field_fetch('ENTRY')[/\S+/]
-      end
-      
-      def name
-        field_fetch('NAME')
-      end
-      
-      def names
-        name.split(', ')
-      end
-      
-      def definition
-        field_fetch('DEFINITION')
-      end
-      
-      def keggclass
-        field_fetch('CLASS')
-      end
-
-      def keggclasses
-        keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
-      end
-      
-      def pathways
-        keggclass.scan(/\[PATH:(.*?)\]/).flatten
-      end
-      
-      def dblinks
-        unless @data['DBLINKS']
-          hash = {}
-          get('DBLINKS').scan(/(\S+):\s*(.*)\n/).each do |k, v|
-            hash[k] = v.split(/\s+/)
-          end
-          @data['DBLINKS'] = hash
-        end
-        @data['DBLINKS']		# Hash of DB:ID in DBLINKS
-      end
-      
-      def genes
-        unless @data['GENES']
-          hash = {}
-          k = ''
-          get('GENES').each_line do |line|
-            line.chomp!
-            line[0, @tagsize] = '' 
-            if line =~ /(\S+):/
-              k = $1
-              hash[k] = []
-            end
-            line[0, 5] = ''
-            line.gsub(/\(\S+/, '').each(' ') do |u|
-              hash[k] << u.strip
-            end
-          end
-          @data['GENES'] = hash
-        end
-        @data['GENES']		# Hash of DB:ID in DBLINKS
-      end
-      
-    end
-    
-  end
-  
-end
-
-
-
-if __FILE__ == $0
-
-  require 'bio/io/fetch'
-
-  flat = Bio::Fetch.query('ko', 'K00001')
-  entry = Bio::KEGG::KO.new(flat)
-
-  p entry.entry_id
-  p entry.name
-  p entry.names
-  p entry.definition
-  p entry.keggclass
-  p entry.keggclasses
-  p entry.pathways
-  p entry.dblinks
-  p entry.genes
-
-end
-
-
-=begin
-
-= Bio::KEGG::KO
-
-KO (KEGG Orthology) entry parser.
-
-* ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
-* ((<URL:ftp://ftp.genome.jp/pub/kegg/tarfiles/ko>))
-
---- Bio::KEGG::KO.new(entry)
-
-Reads a flat file format entry of the KO database.
-
---- Bio::KEGG::KO#entry_id -> String
-
-Returns ID of the entry.
-
---- Bio::KEGG::KO#name -> String
-
-Returns NAME field of the entry.
-
---- Bio::KEGG::KO#names -> Array
-
-Returns an Array of names in NAME field.
-
---- Bio::KEGG::KO#definition -> String
-
-Returns DEFINITION field of the entry.
-
---- Bio::KEGG::KO#keggclass
-
-Returns CLASS field of the entry.
-
---- Bio::KEGG::KO#keggclasses
-
-Returns an Array of biological classes in CLASS field.
-
---- Bio::KEGG::KO#pathways
-
-Returns an Array of KEGG/PATHWAY ID in CLASS field.
-
---- Bio::KEGG::KO#dblinks
-
-Returns a Hash of Array of the database name and entry IDs in DBLINKS field.
-
---- Bio::KEGG::KO#genes
-
-Returns a Hash of Array of the organism ID and entry IDs in GENES field.
-
-=end
-

data/lib/bio/shell/rails/Rakefile

@@ -1,10 +0,0 @@
-# Add your own tasks in files placed in lib/tasks ending in .rake,
-# for example lib/tasks/switchtower.rake, and they will automatically be available to Rake.
-
-require(File.join(File.dirname(__FILE__), 'config', 'boot'))
-
-require 'rake'
-require 'rake/testtask'
-require 'rake/rdoctask'
-
-require 'tasks/rails'