bio-ucsc-api 0.2.0 → 0.2.1

data/lib/bio-ucsc/saccer2/t2micron_est.rb

@@ -0,0 +1,57 @@
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module SacCer2
+
+      class T2micron_est < DBConnection
+        set_table_name "2micron_est"
+ 
+        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 ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+            SQL
+          end
+          cond = {
+            :chrom => interval.chrom,
+            :bins  => Ucsc::UcscBin.bin_all(zstart, zend),
+            :zstart => zstart,
+            :zend => zend,}
+          self.find(first_all,
+                    { :select => "*",
+                      :conditions => [where, cond], })
+        end
+      end # class
+
+    end # module 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/saccer2/t2micron_gap.rb

@@ -0,0 +1,57 @@
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module SacCer2
+
+      class T2micron_gap < DBConnection
+        set_table_name "2micron_gap"
+ 
+        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
+    chrom = :chrom
+AND bin in (:bins)
+AND ((chromStart BETWEEN :zstart AND :zend)
+ OR (chromEnd BETWEEN :zstart AND :zend)
+ OR (chromStart <= :zstart AND chromEnd >= :zend))
+            SQL
+          else
+            where = <<-SQL
+    chrom = :chrom 
+AND ((chromStart BETWEEN :zstart AND :zend)
+AND  (chromEnd BETWEEN :zstart AND :zend))
+            SQL
+          end
+          cond = {
+            :chrom => interval.chrom,
+            :bins  => Ucsc::UcscBin.bin_all(zstart, zend),
+            :zstart => zstart,
+            :zend => zend,}
+          self.find(first_all,
+                    { :select => "*",
+                      :conditions => [where, cond], })
+        end
+      end # class
+
+    end # module 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/saccer2/t2micron_gold.rb

@@ -0,0 +1,58 @@
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module SacCer2
+
+      class T2micron_gold < DBConnection
+        set_table_name "2micron_gold"
+        columns_hash.delete "type"
+
+        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
+    chrom = :chrom
+AND bin in (:bins)
+AND ((chromStart BETWEEN :zstart AND :zend)
+ OR (chromEnd BETWEEN :zstart AND :zend)
+ OR (chromStart <= :zstart AND chromEnd >= :zend))
+            SQL
+          else
+            where = <<-SQL
+    chrom = :chrom 
+AND ((chromStart BETWEEN :zstart AND :zend)
+AND  (chromEnd BETWEEN :zstart AND :zend))
+            SQL
+          end
+          cond = {
+            :chrom => interval.chrom,
+            :bins  => Ucsc::UcscBin.bin_all(zstart, zend),
+            :zstart => zstart,
+            :zend => zend,}
+          self.find(first_all,
+                    { :select => "*",
+                      :conditions => [where, cond], })
+        end
+      end # class
+
+    end # module 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/saccer2/t2micron_intronEst.rb

@@ -0,0 +1,57 @@
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module SacCer2
+
+      class T2micron_intronEst < DBConnection
+        set_table_name "2micron_intronEst"
+ 
+        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 ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+            SQL
+          end
+          cond = {
+            :chrom => interval.chrom,
+            :bins  => Ucsc::UcscBin.bin_all(zstart, zend),
+            :zstart => zstart,
+            :zend => zend,}
+          self.find(first_all,
+                    { :select => "*",
+                      :conditions => [where, cond], })
+        end
+      end # class
+
+    end # module 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/saccer2/t2micron_mrna.rb

@@ -0,0 +1,57 @@
+# Copyright::
+#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+# this table is actually separated
+# into "chr1_*", "chr2_*", etc. This class dynamically
+# define *::Chr1_*, *::Chr2_*, etc. The
+# find_by_interval calls an appropreate class automatically.
+
+module Bio
+  module Ucsc
+    module SacCer2
+
+      class T2micron_mrna < DBConnection
+        set_table_name "2micron_mrna"
+ 
+        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 ((tStart BETWEEN :zstart AND :zend)
+AND  (tEnd BETWEEN :zstart AND :zend))
+            SQL
+          end
+          cond = {
+            :chrom => interval.chrom,
+            :bins  => Ucsc::UcscBin.bin_all(zstart, zend),
+            :zstart => zstart,
+            :zend => zend,}
+          self.find(first_all,
+                    { :select => "*",
+                      :conditions => [where, cond], })
+        end
+      end # class
+
+    end # module 
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/strpur2.rb

@@ -0,0 +1,32 @@
+#
+# = AUTOMATIC Table Definition of the S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) 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__)}/strpur2/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module StrPur2
+      CHROMS = %w() # many scaffolds
+
+      extend TableClassDetector
+
+      base = "#{File.dirname(__FILE__)}/strpur2"
+      # autoload :ChainGalGal3, "#{base}/chaingalgal3"
+      # autoload :ChainGalGal3Link, "#{base}/chaingalgal3link"
+      # autoload :ChainHg18, "#{base}/chainhg18"
+      # autoload :ChainHg18Link, "#{base}/chainhg18link"
+      # autoload :ChainMm9, "#{base}/chainmm9"
+      # autoload :ChainMm9Link, "#{base}/chainmm9link"
+      # autoload :ChainPetMar1, "#{base}/chainpetmar1"
+      # autoload :ChainPetMar1Link, "#{base}/chainpetmar1link"
+      # autoload :Gap, "#{base}/gap"
+      # autoload :Gold, "#{base}/gold"
+      end
+  end
+end

data/lib/bio-ucsc/strpur2/chaingalgal3.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 BraFlo1
+
+      class ChainGalGal3
+        KLASS = "ChainGalGal3"
+        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+
+        Bio::Ucsc::BraFlo1::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/strpur2/chaingalgal3link.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 BraFlo1
+
+      class ChainGalGal3Link
+        KLASS = "ChainGalGal3Link"
+        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
+
+        Bio::Ucsc::BraFlo1::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