bio-twobit 0.2.0 → 0.2.2

data/lib/bio/twobit/references/xentro10.rb

@@ -0,0 +1,16 @@
+require_relative "../reference_genome"
+
+module Bio
+  class TwoBit
+    class XenTro10 < ReferenceGenome
+      def initialize(**kwargs)
+        @metadata      = Metadata.new
+        @metadata.id   = "xenTro10"
+        @metadata.name = "xenTro10"
+        @metadata.url  = "https://hgdownload.soe.ucsc.edu/downloads.html"
+        @data_url      = "https://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/bigZips/xenTro10.2bit"
+        super(**kwargs)
+      end
+    end
+  end
+end

data/lib/bio/twobit/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class TwoBit
-    VERSION = "0.2.0"
+    VERSION = "0.2.2"
   end
 end

data/lib/bio/twobit.rb

@@ -24,22 +24,6 @@ module Bio
         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 @@ module Bio
     end
   end
 end
+
+Dir[__dir__ + "/twobit/references/*.rb"].each { |file| require file }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-twobit
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.2
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-01-11 00:00:00.000000000 Z
+date: 2024-09-19 00:00:00.000000000 Z
 dependencies: []
 description: This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit),
   which provides high-speed access to genomic data in 2bit file format.
@@ -32,21 +32,121 @@ files:
 - lib/bio/twobit/downloader.rb
 - lib/bio/twobit/metadata.rb
 - lib/bio/twobit/reference_genome.rb
+- lib/bio/twobit/references/ailmel1.rb
+- lib/bio/twobit/references/allmis1.rb
+- lib/bio/twobit/references/anocar2.rb
+- lib/bio/twobit/references/anogam3.rb
+- lib/bio/twobit/references/apimel2.rb
+- lib/bio/twobit/references/aplcal1.rb
+- lib/bio/twobit/references/aptman1.rb
+- lib/bio/twobit/references/aquchr2.rb
+- lib/bio/twobit/references/balacu1.rb
+- lib/bio/twobit/references/bostau7.rb
+- lib/bio/twobit/references/braflo1.rb
+- lib/bio/twobit/references/caejap1.rb
+- lib/bio/twobit/references/caepb2.rb
+- lib/bio/twobit/references/caerem3.rb
+- lib/bio/twobit/references/caljac4.rb
+- lib/bio/twobit/references/calmil1.rb
+- lib/bio/twobit/references/canfam4.rb
+- lib/bio/twobit/references/canfam6.rb
+- lib/bio/twobit/references/cb3.rb
+- lib/bio/twobit/references/ce11.rb
+- lib/bio/twobit/references/cersim1.rb
+- lib/bio/twobit/references/chlsab2.rb
+- lib/bio/twobit/references/chohof1.rb
+- lib/bio/twobit/references/chrpic1.rb
+- lib/bio/twobit/references/ci2.rb
+- lib/bio/twobit/references/crigrichov2.rb
 - lib/bio/twobit/references/danrer10.rb
 - lib/bio/twobit/references/danrer11.rb
+- lib/bio/twobit/references/dasnov3.rb
+- lib/bio/twobit/references/dipord1.rb
 - lib/bio/twobit/references/dm6.rb
+- lib/bio/twobit/references/dp3.rb
+- lib/bio/twobit/references/droana2.rb
+- lib/bio/twobit/references/droere1.rb
+- lib/bio/twobit/references/drogri1.rb
+- lib/bio/twobit/references/dromoj2.rb
+- lib/bio/twobit/references/droper1.rb
+- lib/bio/twobit/references/drosec1.rb
+- lib/bio/twobit/references/drosim1.rb
+- lib/bio/twobit/references/drovir2.rb
+- lib/bio/twobit/references/droyak2.rb
+- lib/bio/twobit/references/ebovir3.rb
+- lib/bio/twobit/references/echtel2.rb
+- lib/bio/twobit/references/equcab3.rb
+- lib/bio/twobit/references/erieur2.rb
+- lib/bio/twobit/references/felcat9.rb
+- lib/bio/twobit/references/fr2.rb
+- lib/bio/twobit/references/gadmor1.rb
+- lib/bio/twobit/references/galgal6.rb
+- lib/bio/twobit/references/geofor1.rb
+- lib/bio/twobit/references/gorgor6.rb
+- lib/bio/twobit/references/hetgla2.rb
 - lib/bio/twobit/references/hg19.rb
 - lib/bio/twobit/references/hg38.rb
 - lib/bio/twobit/references/hs1.rb
+- lib/bio/twobit/references/latcha1.rb
+- lib/bio/twobit/references/loxafr3.rb
+- lib/bio/twobit/references/maceug2.rb
+- lib/bio/twobit/references/macfas5.rb
+- lib/bio/twobit/references/manpen1.rb
+- lib/bio/twobit/references/melgal1.rb
+- lib/bio/twobit/references/melund1.rb
+- lib/bio/twobit/references/micmur2.rb
 - lib/bio/twobit/references/mm10.rb
 - lib/bio/twobit/references/mm39.rb
 - lib/bio/twobit/references/mm9.rb
+- lib/bio/twobit/references/mondom5.rb
+- lib/bio/twobit/references/myoluc2.rb
+- lib/bio/twobit/references/nanpar1.rb
+- lib/bio/twobit/references/naslar1.rb
+- lib/bio/twobit/references/neosch1.rb
+- lib/bio/twobit/references/nomleu3.rb
+- lib/bio/twobit/references/ochpri3.rb
+- lib/bio/twobit/references/orenil2.rb
+- lib/bio/twobit/references/ornana2.rb
+- lib/bio/twobit/references/orycun2.rb
+- lib/bio/twobit/references/orylat2.rb
+- lib/bio/twobit/references/otogar3.rb
+- lib/bio/twobit/references/oviari4.rb
+- lib/bio/twobit/references/panpan3.rb
+- lib/bio/twobit/references/pantro6.rb
+- lib/bio/twobit/references/papanu4.rb
+- lib/bio/twobit/references/papham1.rb
+- lib/bio/twobit/references/petmar3.rb
+- lib/bio/twobit/references/ponabe2.rb
+- lib/bio/twobit/references/ponabe3.rb
+- lib/bio/twobit/references/pripac1.rb
+- lib/bio/twobit/references/procap1.rb
+- lib/bio/twobit/references/ptevam1.rb
+- lib/bio/twobit/references/rhemac10.rb
+- lib/bio/twobit/references/rn6.rb
+- lib/bio/twobit/references/saccer3.rb
+- lib/bio/twobit/references/saibol1.rb
+- lib/bio/twobit/references/sarhar1.rb
+- lib/bio/twobit/references/sorara2.rb
+- lib/bio/twobit/references/spetri2.rb
+- lib/bio/twobit/references/strpur2.rb
+- lib/bio/twobit/references/susscr11.rb
+- lib/bio/twobit/references/taegut2.rb
+- lib/bio/twobit/references/tarsyr2.rb
+- lib/bio/twobit/references/tetnig2.rb
+- lib/bio/twobit/references/thasir1.rb
+- lib/bio/twobit/references/triman1.rb
+- lib/bio/twobit/references/tupbel1.rb
+- lib/bio/twobit/references/turtru2.rb
+- lib/bio/twobit/references/uusfur1.rb
+- lib/bio/twobit/references/vicpac2.rb
+- lib/bio/twobit/references/wuhcor1.rb
+- lib/bio/twobit/references/xentro10.rb
 - lib/bio/twobit/version.rb
-homepage: https://github.com/ruby-on-bioc/bio-twobit
+homepage: https://github.com/kojix2/bio-twobit
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -61,8 +161,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.1
-signing_key: 
+rubygems_version: 3.5.16
+signing_key:
 specification_version: 4
 summary: A ruby library for accessing 2bit files
 test_files: []