bio-ucsc-api 0.2.0 → 0.2.1

data/lib/bio-ucsc/galgal3/mrna.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 GalGal3
+
+      class Mrna
+        KLASS = "Mrna"
+        KLASS_S = "mrna"
+
+        Bio::Ucsc::GalGal3::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
+
+              def self.find_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt)
+                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})
+          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})
+          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/rmsk.rb

@@ -0,0 +1,78 @@
+# = rmsk.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, the Rmsk table is actually separated
+# into "chr1_rmsk", "chr2_rmsk", etc. The Rmsk class dynamically
+# define Rmsk::Chr1_Rmsk, Rmsk::Chr2_Rmsk, etc. The
+# Rmsk.find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module GalGal3
+
+      class Rmsk
+        Bio::Ucsc::GalGal3::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
+
+              def self.find_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt)
+                zstart = interval.zero_start
+                zend   = interval.zero_end
+                if opt[:partial] == true
+                  where = <<-SQL
+      genoName = :chrom
+AND   bin in (:bins)
+AND ((genoStart BETWEEN :zstart AND :zend)
+ OR  (genoEnd BETWEEN :zstart AND :zend)
+ OR  (genoStart <= :zstart AND genoEnd >= :zend))
+                  SQL
+                else
+                  where = <<-SQL
+      genoName = :chrom
+AND   bin in (:bins)
+AND ((genoStart BETWEEN :zstart AND :zend)
+AND  (genoEnd 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})
+          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})
+          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)
+        end
+      end # class Rmsk
+
+    end # module 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/gasacu1.rb

@@ -0,0 +1,39 @@
+#
+# = AUTOMATIC Table Definition of the Stickleback Feb. 2006 (Broad/gasAcu1) 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__)}/gasacu1/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module GasAcu1
+      CHROMS = 
+%w(chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII chrIX chrX
+chrXI chrXII chrXIII chrXIV chrXV chrXVI chiXVII chrXVIII chrXIX chrXX
+chrXXI chrM)
+
+      extend TableClassDetector
+
+      base = "#{File.dirname(__FILE__)}/gasacu1"
+      autoload :ChainAnoCar1, "#{base}/chainanocar1"
+      autoload :ChainAnoCar1Link, "#{base}/chainanocar1link"
+      autoload :ChainFr2, "#{base}/chainfr2"
+      autoload :ChainFr2Link, "#{base}/chainfr2link"
+      autoload :ChainGalGal3, "#{base}/chaingalgal3"
+      autoload :ChainGalGal3Link, "#{base}/chaingalgal3link"
+      autoload :ChainMm9, "#{base}/chainmm9"
+      autoload :ChainMm9Link, "#{base}/chainmm9link"
+      autoload :ChainOryLat2, "#{base}/chainorylat2"
+      autoload :ChainOryLat2Link, "#{base}/chainorylat2link"
+      autoload :Est, "#{base}/est"
+      autoload :IntronEst, "#{base}/intronest"
+      autoload :Mrna, "#{base}/mrna"
+      autoload :Rmsk, "#{base}/rmsk"
+    end
+  end
+end

data/lib/bio-ucsc/gasacu1/chainanocar1.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 GasAcu1
+
+      class ChainAnoCar1
+        KLASS = "ChainAnoCar1"
+        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+
+        Bio::Ucsc::GasAcu1::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
+
+              def self.find_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt)
+                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})
+          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})
+          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/gasacu1/chainanocar1link.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 GasAcu1
+
+      class ChainAnoCar1Link
+        KLASS = "ChainAnoCar1Link"
+        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+
+        Bio::Ucsc::GasAcu1::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
+
+              def self.find_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt)
+                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})
+          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})
+          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/gasacu1/chainfr2.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 GasAcu1
+
+      class ChainFr2
+        KLASS = "ChainFr2"
+        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+
+        Bio::Ucsc::GasAcu1::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
+
+              def self.find_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt)
+                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})
+          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})
+          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/gasacu1/chainfr2link.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 GasAcu1
+
+      class ChainFr2Link
+        KLASS = "ChainFr2Link"
+        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+
+        Bio::Ucsc::GasAcu1::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
+
+              def self.find_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :first, opt)
+              end
+        
+              def self.find_all_by_interval(interval, opt = {:partial => true})
+                find_first_or_all_by_interval(interval, :all, opt)
+              end
+
+              def self.find_first_or_all_by_interval(interval, first_all, opt)
+                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})
+          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})
+          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