bio-ucsc-api 0.5.2 → 0.5.3

data/lib/bio-ucsc/galgal3.rb

@@ -1,56 +0,0 @@
-#
-# = AUTOMATIC Table Definition of the Chicken May 2006 (WUGSC 2.1/galGal3) assembly
-# 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__)}/table_class_detector"
-
-module Bio
-  module Ucsc
-    module GalGal3
-      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 chr25 chr26 chr27 chr28 chr32 chrW chrZ)
-
-      extend TableClassDetector
-      include DBConnector
-      DBConnection.database "galGal3"
- 
-      base = "#{::File.dirname(__FILE__)}/galgal3"
-      autoload :ChainAnoCar1, "#{base}/chainanocar1"
-      autoload :ChainAnoCar1Link, "#{base}/chainanocar1link"
-      autoload :ChainBraFlo1, "#{base}/chainbraflo1"
-      autoload :ChainBraFlo1Link, "#{base}/chainbraflo1link"
-      autoload :ChainCavPor3, "#{base}/chaincavpor3"
-      autoload :ChainCavPor3Link, "#{base}/chaincavpor3link"
-      autoload :ChainDanRer4, "#{base}/chaindanrer4"
-      autoload :ChainDanRer4Link, "#{base}/chaindanrer4link"
-      autoload :ChainFr2, "#{base}/chainfr2"
-      autoload :ChainFr2Link, "#{base}/chainfr2link"
-      autoload :ChainGasAcu1, "#{base}/chaingasacu1"
-      autoload :ChainGasAcu1Link, "#{base}/chaingasacu1link"
-      autoload :ChainMm9, "#{base}/chainmm9"
-      autoload :ChainMm9Link, "#{base}/chainmm9link"
-      autoload :ChainOrnAna1, "#{base}/chainornana1"
-      autoload :ChainOrnAna1Link, "#{base}/chainornana1link"
-      autoload :ChainPetMar1, "#{base}/chainpetmar1"
-      autoload :ChainPetMar1Link, "#{base}/chainpetmar1link"
-      autoload :ChainRn4, "#{base}/chainrn4"
-      autoload :ChainRn4Link, "#{base}/chainrn4link"
-      autoload :ChainTaeGut1, "#{base}/chaintaegut1"
-      autoload :ChainTaeGut1Link, "#{base}/chaintaegut1link"
-      autoload :ChainXenTro2, "#{base}/chainxentro2"
-      autoload :ChainXenTro2Link, "#{base}/chainxentro2link"
-      autoload :Est, "#{base}/est"
-      autoload :Gap, "#{base}/gap"
-      autoload :Gold, "#{base}/gold"
-      autoload :IntronEst, "#{base}/intronest"
-      autoload :Mrna, "#{base}/mrna"
-      autoload :Rmsk, "#{base}/rmsk"
-    end
-  end
-end

data/lib/bio-ucsc/galgal3/chainanocar1.rb

@@ -1,84 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module GalGal3
-
-      class ChainAnoCar1
-        include DBConnector
-        DBConnection.database "galGal3"
-
-        KLASS = "ChainAnoCar1"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              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}); 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}); 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); interval =  Bio::Ucsc::Gi.wrap(interval)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        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}); 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)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/galgal3/chainanocar1link.rb

@@ -1,84 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module GalGal3
-
-      class ChainAnoCar1Link
-        include DBConnector
-        DBConnection.database "galGal3"
-
-        KLASS = "ChainAnoCar1Link"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              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}); 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}); 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); interval =  Bio::Ucsc::Gi.wrap(interval)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        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}); 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)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/galgal3/chainbraflo1.rb

@@ -1,84 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module GalGal3
-
-      class ChainBraFlo1
-        include DBConnector
-        DBConnection.database "galGal3"
-
-        KLASS = "ChainBraFlo1"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              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}); 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}); 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); interval =  Bio::Ucsc::Gi.wrap(interval)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        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}); 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)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/galgal3/chainbraflo1link.rb

@@ -1,84 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module GalGal3
-
-      class ChainBraFlo1Link
-        include DBConnector
-        DBConnection.database "galGal3"
-
-        KLASS = "ChainBraFlo1Link"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              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}); 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}); 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); interval =  Bio::Ucsc::Gi.wrap(interval)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        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}); 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)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/galgal3/chaincavpor3link.rb

@@ -1,84 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module GalGal3
-
-      class ChainCavPor3Link
-        include DBConnector
-        DBConnection.database "galGal3"
-
-        KLASS = "ChainCavPor3Link"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              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}); 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}); 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); interval =  Bio::Ucsc::Gi.wrap(interval)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        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}); 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)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio