bio-ucsc-api 0.5.2 → 0.5.3

data/lib/bio-ucsc/hgfixed.rb

@@ -6,7 +6,6 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{::File.dirname(__FILE__)}/db_connector"
 require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio

data/lib/bio-ucsc/rn5.rb

@@ -0,0 +1,66 @@
+#
+# = AUTOMATIC Table Definition of the Rat Rn5 assembly
+# Copyright::   Copyright (C) 2011, 2012, 2013
+#               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 Rn5
+      CHROMS = 
+%w(chrM chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10
+chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
+chrX)
+      extend TableClassDetector
+
+      def self.default
+        DBConnection.default
+      end
+
+      def self.connect(param = Hash.new)
+        DBConnection.db_adapter = param[:db_adapter] if param[:db_adapter]
+        DBConnection.db_host = param[:db_host] if param[:db_host]
+        DBConnection.db_username = param[:db_username] if param[:db_username]
+        DBConnection.password = param[:password] if param[:password]
+        DBConnection.connect
+      end
+
+      class DBConnection < ActiveRecord::Base
+        include SafeAttributes
+        self.inheritance_column = 'dummy_not_to_use'
+
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+        @@db_name     ||= 'rn5'
+
+        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 => @@db_name,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end # class DBConnection
+
+      base = "#{::File.dirname(__FILE__)}/rn4"
+      #
+    end
+  end
+end

data/lib/bio-ucsc/rn5/chaincanfam2.rb

@@ -0,0 +1,82 @@
+# = chaincanfam2.rb
+# 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 Rn4
+
+      class ChainCanFam2
+        KLASS = "ChainCanFam2"
+        KLASS_S = "chainCanFam2"
+
+         Bio::Ucsc::Rn4::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/chainmm9link.rb → rn5/chaincanfam2link.rb}

@@ -1,3 +1,4 @@
+# = chainbraflo1link.rb
 # Copyright::
 #  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
@@ -9,16 +10,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
-      class ChainMm9Link
-        include DBConnector
-        DBConnection.database "galGal3"
+      class ChainCanFam2Link
+        KLASS = "ChainCanFam2Link"
+        KLASS_S = "chainCanFam2Link"
 
-        KLASS = "ChainMm9Link"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+         Bio::Ucsc::Rn4::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}"
@@ -73,7 +71,7 @@ AND  (tEnd BETWEEN :zstart AND :zend))
         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]
+         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

data/lib/bio-ucsc/{galgal3 → rn5}/chaincavpor3.rb

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class ChainCavPor3
-        include DBConnector
-        DBConnection.database "galGal3"
-
         KLASS = "ChainCavPor3"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+        KLASS_S = "chainCavPor3"
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::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}"

data/lib/bio-ucsc/rn5/chaincavpor3link.rb

@@ -0,0 +1,81 @@
+# 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 Rn4
+
+      class ChainCavPor3Link
+        KLASS = "ChainCavPor3Link"
+        KLASS_S = "chainCavPor3Link"
+
+        Bio::Ucsc::Rn4::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 → rn5}/chaindanrer4.rb

@@ -9,16 +9,13 @@
 
 module Bio
   module Ucsc
-    module GalGal3
+    module Rn4
 
       class ChainDanRer4
-        include DBConnector
-        DBConnection.database "galGal3"
-
         KLASS = "ChainDanRer4"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+        KLASS_S = "chainDanRer4"
 
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
+        Bio::Ucsc::Rn4::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}"

data/lib/bio-ucsc/rn5/chaindanrer4link.rb

@@ -0,0 +1,81 @@
+# 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 Rn4
+
+      class ChainDanRer4Link
+        KLASS = "ChainDanRer4Link"
+        KLASS_S = "chainDanRer4Link"
+
+        Bio::Ucsc::Rn4::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/rn5/chainequcab1.rb

@@ -0,0 +1,81 @@
+# 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 Rn4
+
+      class ChainEquCab1
+        KLASS = "ChainEquCab1"
+        KLASS_S = "chainEquCab1"
+
+        Bio::Ucsc::Rn4::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