bio-ucsc-api 0.2.0 → 0.2.1

data/lib/bio-ucsc/mm9/mrna.rb

@@ -56,8 +56,8 @@ AND  (tEnd BETWEEN :zstart AND :zend))
                   :zend   => zend,
                 }
                 self.find(first_all,
-                          :select => "*",
-                          :conditions => [where, cond],)
+                          { :select => "*",
+                            :conditions => [where, cond], })
               end
             end
           !

data/lib/bio-ucsc/mm9/rmsk.rb

@@ -53,8 +53,8 @@ AND  (genoEnd BETWEEN :zstart AND :zend))
                   :zend   => zend,
                 }
                 self.find(first_all,
-                          :select => "*",
-                          :conditions => [where, cond],)
+                          { :select => "*",
+                            :conditions => [where, cond], })
               end
             end
           !

data/lib/bio-ucsc/mondom5.rb

@@ -0,0 +1,21 @@
+#
+# = AUTOMATIC Table Definition of the Opossum Oct. 2006 (Broad/monDom5) assembly
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/mondom5/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module MonDom5
+      CHROMS = 
+%w(Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 ChrX ChrM)
+      extend TableClassDetector
+      base = "#{File.dirname(__FILE__)}/mondom5"
+    end
+  end
+end

data/lib/bio-ucsc/mondom5/db_connection.rb

@@ -0,0 +1,57 @@
+#
+# = db_connection.rb
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2010
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module MonDom5
+      DATABASE_NAME = "monDom5"
+
+      # = DESCRIPTION
+      # Actual connection established to the UCSC mysql server.
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The #connect method make the connection
+        #
+        # = USAGE
+        #  Bin::Ucsc::DB_NAME::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => DATABASE_NAME,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end
+    end # module
+    
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/ornana1.rb

@@ -0,0 +1,20 @@
+#
+# = AUTOMATIC Table Definition of the Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1)
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/ornana1/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module OrnAna1
+      CHROMS = %w() # many scaffolds
+      extend TableClassDetector
+      base = "#{File.dirname(__FILE__)}/ornana1"
+    end
+  end
+end

data/lib/bio-ucsc/ornana1/db_connection.rb

@@ -0,0 +1,57 @@
+#
+# = db_connection.rb
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2010
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module OrnAna1
+      DATABASE_NAME = "ornAna1"
+
+      # = DESCRIPTION
+      # Actual connection established to the UCSC mysql server.
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The #connect method make the connection
+        #
+        # = USAGE
+        #  Bin::Ucsc::DB_NAME::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => DATABASE_NAME,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end
+    end # module
+    
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/orycun2.rb

@@ -0,0 +1,24 @@
+#
+# = AUTOMATIC Table Definition of the Rabbit Apr. 2009 (Broad/oryCun2) assembly
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/orycun2/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module OryCun2
+      CHROMS =
+%w(Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9
+Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19
+Chr20 Chr21 ChrX)
+      extend TableClassDetector
+
+      base = "#{File.dirname(__FILE__)}/orycun2"
+    end
+  end
+end

data/lib/bio-ucsc/orycun2/db_connection.rb

@@ -0,0 +1,57 @@
+#
+# = db_connection.rb
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2010
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module OryCun2
+      DATABASE_NAME = "oryCun2"
+
+      # = DESCRIPTION
+      # Actual connection established to the UCSC mysql server.
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The #connect method make the connection
+        #
+        # = USAGE
+        #  Bin::Ucsc::DB_NAME::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => DATABASE_NAME,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end
+    end # module
+    
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/orylat2.rb

@@ -0,0 +1,24 @@
+#
+# = AUTOMATIC Table Definition of the Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/orylat2/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module OryLat2
+      CHROMS = 
+%w(chrM chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10
+chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
+chr21 chr22 chr23 chr24)
+      extend TableClassDetector
+
+      base = "#{File.dirname(__FILE__)}/orylat2"
+    end
+  end
+end

data/lib/bio-ucsc/orylat2/db_connection.rb

@@ -0,0 +1,55 @@
+#
+# = db_connection.rb - UCSC DB connection
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2010
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module OryLat2
+      # = DESCRIPTION
+      # Actual connection established to the UCSC mysql server.
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The #connect method make the connection
+        #
+        # = USAGE
+        #  Bin::Ucsc::DB_NAME::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => 'oryLat2',
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end
+    end # module
+    
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/oviari1.rb

@@ -0,0 +1,24 @@
+#
+# = AUTOMATIC Table Definition of the Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/oviari1/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module OviAri1
+      CHROMS =
+%w(Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9
+Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 Chr20
+Chr21 Chr22 Chr23 Chr24 Chr25 Chr26 ChrX)
+      extend TableClassDetector
+
+      base = "#{File.dirname(__FILE__)}/oviari1"
+    end
+  end
+end

data/lib/bio-ucsc/oviari1/db_connection.rb

@@ -0,0 +1,57 @@
+#
+# = db_connection.rb
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2010
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module OviAri1
+      DATABASE_NAME = "oviAri1"
+
+      # = DESCRIPTION
+      # Actual connection established to the UCSC mysql server.
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The #connect method make the connection
+        #
+        # = USAGE
+        #  Bin::Ucsc::DB_NAME::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => DATABASE_NAME,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end
+    end # module
+    
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/pantro3.rb

@@ -0,0 +1,24 @@
+#
+# = AUTOMATIC Table Definition of the Chimp Oct. 2010 (CGSC 2.1.3/panTro3) assembly
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/pantro3/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module PanTro3
+      CHROMS = 
+%w(chrM chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10
+chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
+chr21 chr22 chrX chrY)
+      extend TableClassDetector
+
+      base = "#{File.dirname(__FILE__)}/pantro3"
+    end
+  end
+end