Add UCSC reference genomes

lib/bio/twobit.rb

@@ -24,22 +24,6 @@ def open(*args, **kwargs)
         end
         file
       end
-
-      # Here, const_missing is used instead of autoload.
-
-      def const_missing(name)
-        # prevents const_get from being called recursively many times.
-        @missing_const ||= []
-        super if @missing_const.include? name
-        @missing_const << name
-
-        path = File.join(__dir__, "twobit/references", "#{name.to_s.downcase}.rb")
-        if File.exist?(path)
-          require path
-          return const_get(name)
-        end
-        super
-      end
     end
 
     def initialize(fname, masked: false)
@@ -117,3 +101,5 @@ def download(output_path, url)
     end
   end
 end
+
+Dir[__dir__ + "/twobit/references/*.rb"].each { |file| require file }

lib/bio/twobit/references/ailmel1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AilMel1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "ailMel1"
+        @metadata.name = "ailMel1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/ailMel1/bigZips/ailMel1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/allmis1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AllMis1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "allMis1"
+        @metadata.name = "allMis1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/allMis1/bigZips/allMis1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/anocar2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AnoCar2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "anoCar2"
+        @metadata.name = "anoCar2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/anoCar2/bigZips/anoCar2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/anogam3.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AnoGam3 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "anoGam3"
+        @metadata.name = "anoGam3"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/anoGam3/bigZips/anoGam3.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/apimel2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class ApiMel2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "apiMel2"
+        @metadata.name = "apiMel2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/apiMel2/bigZips/apiMel2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/aplcal1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AplCal1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "aplCal1"
+        @metadata.name = "aplCal1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/aplCal1/bigZips/aplCal1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/aptman1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AptMan1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "aptMan1"
+        @metadata.name = "aptMan1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/aptMan1/bigZips/aptMan1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/aquchr2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class AquChr2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "aquChr2"
+        @metadata.name = "aquChr2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/aquChr2/bigZips/aquChr2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/balacu1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class BalAcu1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "balAcu1"
+        @metadata.name = "balAcu1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/balAcu1/bigZips/balAcu1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/bostau7.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class BosTau7 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "bosTau7"
+        @metadata.name = "bosTau7"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau7/bigZips/bosTau7.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/braflo1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class BraFlo1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "braFlo1"
+        @metadata.name = "braFlo1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/braFlo1/bigZips/braFlo1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/caejap1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CaeJap1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "caeJap1"
+        @metadata.name = "caeJap1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/caeJap1/bigZips/caeJap1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/caepb2.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CaePb2 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "caePb2"
+        @metadata.name = "caePb2"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/caePb2/bigZips/caePb2.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/caerem3.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CaeRem3 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "caeRem3"
+        @metadata.name = "caeRem3"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/caeRem3/bigZips/caeRem3.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/caljac4.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CalJac4 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "calJac4"
+        @metadata.name = "calJac4"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/calJac4/bigZips/calJac4.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/calmil1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CalMil1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "calMil1"
+        @metadata.name = "calMil1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/calMil1/bigZips/calMil1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/canfam4.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CanFam4 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "canFam4"
+        @metadata.name = "canFam4"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/canfam6.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CanFam6 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "canFam6"
+        @metadata.name = "canFam6"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/cb3.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Cb3 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "cb3"
+        @metadata.name = "cb3"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/cb3/bigZips/cb3.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/ce11.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class Ce11 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "ce11"
+        @metadata.name = "ce11"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

lib/bio/twobit/references/cersim1.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class CerSim1 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "cerSim1"
+        @metadata.name = "cerSim1"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/cerSim1/bigZips/cerSim1.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end