bio-ucsc-api 0.3.1 → 0.4.0

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

@@ -13,21 +13,24 @@ module Bio
     module Mm9
 
       class Rmsk
+        include DBConnector
+        DBConnection.database "mm9"
+ 
         Bio::Ucsc::Mm9::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_Rmsk < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
-              set_primary_key nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_rmsk"
+              self.primary_key = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true
@@ -60,13 +63,13 @@ AND  (genoEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_Rmsk")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_Rmsk")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/mondom5.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the Opossum Oct. 2006 (Broad/monDom5) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               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"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -15,7 +15,10 @@ module Bio
       CHROMS = 
 %w(Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 ChrX ChrM)
       extend TableClassDetector
-      base = "#{File.dirname(__FILE__)}/mondom5"
+      include DBConnector
+      DBConnection.database "monDom5"
+
+      base = "#{::File.dirname(__FILE__)}/mondom5"
     end
   end
 end

data/lib/bio-ucsc/ornana1.rb

@@ -6,15 +6,18 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/ornana1/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
     module OrnAna1
       CHROMS = %w() # many scaffolds
       extend TableClassDetector
-      base = "#{File.dirname(__FILE__)}/ornana1"
+      include DBConnector
+      DBConnection.database "ornAna1"
+
+      base = "#{::File.dirname(__FILE__)}/ornana1"
     end
   end
 end

data/lib/bio-ucsc/orycun2.rb

@@ -6,8 +6,8 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/orycun2/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -17,8 +17,10 @@ module Bio
 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19
 Chr20 Chr21 ChrX)
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "oryCun2"
 
-      base = "#{File.dirname(__FILE__)}/orycun2"
+      base = "#{::File.dirname(__FILE__)}/orycun2"
     end
   end
 end

data/lib/bio-ucsc/orylat2.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               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"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -17,8 +17,10 @@ module Bio
 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
 chr21 chr22 chr23 chr24)
       extend TableClassDetector
-
-      base = "#{File.dirname(__FILE__)}/orylat2"
+      include DBConnector
+      DBConnection.database "oryLat2"
+ 
+      base = "#{::File.dirname(__FILE__)}/orylat2"
     end
   end
 end

data/lib/bio-ucsc/oviari1.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               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"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -17,8 +17,10 @@ module Bio
 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 Chr20
 Chr21 Chr22 Chr23 Chr24 Chr25 Chr26 ChrX)
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "oviAri1"
 
-      base = "#{File.dirname(__FILE__)}/oviari1"
+      base = "#{::File.dirname(__FILE__)}/oviari1"
     end
   end
 end

data/lib/bio-ucsc/pantro3.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the Chimp Oct. 2010 (CGSC 2.1.3/panTro3) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               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"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -17,8 +17,10 @@ module Bio
 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
 chr21 chr22 chrX chrY)
       extend TableClassDetector
-
-      base = "#{File.dirname(__FILE__)}/pantro3"
+      include DBConnector
+      DBConnection.database "panTro3"
+      
+      base = "#{::File.dirname(__FILE__)}/pantro3"
     end
   end
 end

data/lib/bio-ucsc/petmar1.rb

@@ -1,22 +1,23 @@
 #
 # = AUTOMATIC Table Definition of the Lamprey Mar. 2007 (WUGSC 3.0/petMar1) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/petmar1/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
     module PetMar1
       CHROMS = %() # many contigs
-
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "petMar1"
 
-      base = "#{File.dirname(__FILE__)}/gasacu1"
+      base = "#{::File.dirname(__FILE__)}/petMar1"
     end
   end
 end

data/lib/bio-ucsc/ponabe2.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/ponabe2/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -17,8 +17,10 @@ module Bio
 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19
 Chr20 Chr21 Chr22 ChrX ChrY)
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "ponAbe2"
 
-      base = "#{File.dirname(__FILE__)}/ponabe2"
+      base = "#{::File.dirname(__FILE__)}/ponabe2"
       autoload :ChainMm9, "#{base}/chainmm9"
       autoload :ChainMm9Link, "#{base}/chainmm9link"
       autoload :ChainOrnAna1, "#{base}/chainornana1"

data/lib/bio-ucsc/ponabe2/chainmm9.rb

@@ -12,25 +12,28 @@ module Bio
     module PonAbe2
 
       class ChainMm9
+        include DBConnector
+        DBConnection.database "ponAbe1"
+         
         KLASS = "ChainMm9"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::PonAbe2::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/ponabe2/chainmm9link.rb

@@ -12,25 +12,28 @@ module Bio
     module PonAbe2
 
       class ChainMm9Link
+        include DBConnector
+        DBConnection.database "ponAbe1"
+         
         KLASS = "ChainMm9Link"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::PonAbe2::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/ponabe2/chainornana1.rb

@@ -12,25 +12,28 @@ module Bio
     module PonAbe2
 
       class ChainOrnAna1
+        include DBConnector
+        DBConnection.database "ponAbe1"
+         
         KLASS = "ChainOrnAna1"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::PonAbe2::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/ponabe2/chainornana1link.rb

@@ -12,25 +12,28 @@ module Bio
     module PonAbe2
 
       class ChainOrnAna1Link
+        include DBConnector
+        DBConnection.database "ponAbe1"
+         
         KLASS = "ChainOrnAna1Link"
         KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
 
         Bio::Ucsc::PonAbe2::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)