bio-ucsc-api 0.6.2 → 0.6.3

checksums.yaml

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data/ChangeLog.md

@@ -1,4 +1,5 @@
 #Change Log
+ * **BUG-FIX** (v.0.6.3) Bio::Ucsc::File::TwoBit#find_by_interval fails in retrieving reference sequences including entire "N" blocks, e.g. "aaaNNttt".
  * **BUG-FIX** (v.0.6.2) NoMemoryError in Bio::Ucsc::File::Twobit.open. Now internally File.open is used instead of Kernel.open.
  * **UPDATE** (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions.
  * **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies.

data/Gemfile

@@ -12,11 +12,11 @@ gem "bio-genomic-interval",            ">= 0.1.2"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rake",    "~> 10.1.0" 
-  gem "rspec",   "~> 2.14.1"
-  gem "bundler", "~> 1.3.5"
-  gem "jeweler", "~> 1.8.8"
-  gem "bio",     ">= 1.4.3"
+  gem "rake",    ">= 10.1.0" 
+  gem "rspec",   ">= 2.14.1"
+  gem "bundler", ">= 1.3.5"
+  gem "jeweler", ">= 2.3.7"
+  gem "bio",     ">= 1.5.1"
   gem "rdoc",    ">= 4.0.1"
   # gem "simplecov", :require => false, :group => :test
 end  

data/Gemfile.lock

@@ -1,87 +1,96 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activemodel (4.0.3)
-      activesupport (= 4.0.3)
+    activemodel (4.0.13)
+      activesupport (= 4.0.13)
       builder (~> 3.1.0)
-    activerecord (4.0.3)
-      activemodel (= 4.0.3)
+    activerecord (4.0.13)
+      activemodel (= 4.0.13)
       activerecord-deprecated_finders (~> 1.0.2)
-      activesupport (= 4.0.3)
+      activesupport (= 4.0.13)
       arel (~> 4.0.0)
-    activerecord-deprecated_finders (1.0.3)
-    activesupport (4.0.3)
-      i18n (~> 0.6, >= 0.6.4)
+    activerecord-deprecated_finders (1.0.4)
+    activesupport (4.0.13)
+      i18n (~> 0.6, >= 0.6.9)
       minitest (~> 4.2)
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.3.5)
+    addressable (2.4.0)
     arel (4.0.2)
-    atomic (1.1.15)
-    atomic (1.1.15-java)
-    bio (1.4.3.0001)
+    bio (1.5.1)
     bio-genomic-interval (0.1.2)
     builder (3.1.4)
-    diff-lcs (1.2.5)
-    faraday (0.8.9)
-      multipart-post (~> 1.2.0)
-    git (1.2.6)
-    github_api (0.10.1)
-      addressable
-      faraday (~> 0.8.1)
-      hashie (>= 1.2)
-      multi_json (~> 1.4)
-      nokogiri (~> 1.5.2)
-      oauth2
-    hashie (2.0.5)
-    highline (1.6.21)
-    i18n (0.6.9)
-    jeweler (1.8.8)
+    descendants_tracker (0.0.4)
+      thread_safe (~> 0.3, >= 0.3.1)
+    diff-lcs (1.3)
+    faraday (0.9.2)
+      multipart-post (>= 1.2, < 3)
+    git (1.3.0)
+    github_api (0.16.0)
+      addressable (~> 2.4.0)
+      descendants_tracker (~> 0.0.4)
+      faraday (~> 0.8, < 0.10)
+      hashie (>= 3.4)
+      mime-types (>= 1.16, < 3.0)
+      oauth2 (~> 1.0)
+    hashie (3.5.6)
+    highline (1.7.8)
+    i18n (0.8.6)
+    jar-dependencies (0.3.11)
+    jeweler (2.3.7)
       builder
-      bundler (~> 1.0)
+      bundler (>= 1)
       git (>= 1.2.5)
-      github_api (= 0.10.1)
+      github_api (~> 0.16.0)
       highline (>= 1.6.15)
-      nokogiri (= 1.5.10)
+      nokogiri (>= 1.5.10)
+      psych (~> 2.2)
       rake
       rdoc
-    json (1.8.1)
-    json (1.8.1-java)
-    jwt (0.1.11)
-      multi_json (>= 1.5)
+      semver2
+    jwt (1.5.6)
+    mime-types (2.99.3)
+    mini_portile2 (2.2.0)
     minitest (4.7.5)
-    multi_json (1.9.0)
-    multi_xml (0.5.5)
-    multipart-post (1.2.0)
+    multi_json (1.12.1)
+    multi_xml (0.6.0)
+    multipart-post (2.0.0)
     mysql (2.9.1)
-    nokogiri (1.5.10)
-    nokogiri (1.5.10-java)
-    oauth2 (0.9.3)
-      faraday (>= 0.8, < 0.10)
-      jwt (~> 0.1.8)
+    nokogiri (1.8.0)
+      mini_portile2 (~> 2.2.0)
+    nokogiri (1.8.0-java)
+    oauth2 (1.4.0)
+      faraday (>= 0.8, < 0.13)
+      jwt (~> 1.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
-      rack (~> 1.2)
-    rack (1.5.2)
-    rake (10.1.1)
-    rdoc (4.1.1)
-      json (~> 1.4)
-    rspec (2.14.1)
-      rspec-core (~> 2.14.0)
-      rspec-expectations (~> 2.14.0)
-      rspec-mocks (~> 2.14.0)
-    rspec-core (2.14.8)
-    rspec-expectations (2.14.5)
-      diff-lcs (>= 1.1.3, < 2.0)
-    rspec-mocks (2.14.6)
+      rack (>= 1.2, < 3)
+    psych (2.2.4)
+    psych (2.2.4-java)
+      jar-dependencies (>= 0.1.7)
+    rack (2.0.3)
+    rake (12.0.0)
+    rdoc (5.1.0)
+    rspec (3.6.0)
+      rspec-core (~> 3.6.0)
+      rspec-expectations (~> 3.6.0)
+      rspec-mocks (~> 3.6.0)
+    rspec-core (3.6.0)
+      rspec-support (~> 3.6.0)
+    rspec-expectations (3.6.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.6.0)
+    rspec-mocks (3.6.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.6.0)
+    rspec-support (3.6.0)
     safe_attributes (1.0.10)
       activerecord (>= 3.0.0)
-    thread_safe (0.2.0)
-      atomic (>= 1.1.7, < 2)
-    thread_safe (0.2.0-java)
-      atomic (>= 1.1.7, < 2)
-    tzinfo (0.3.39)
+    semver2 (3.4.2)
+    thread_safe (0.3.6)
+    thread_safe (0.3.6-java)
+    tzinfo (0.3.53)
 
 PLATFORMS
   java
@@ -91,12 +100,15 @@ DEPENDENCIES
   activerecord (~> 4.0.2)
   activerecord-deprecated_finders (~> 1.0.3)
   activesupport (~> 4.0.2)
-  bio (>= 1.4.3)
+  bio (>= 1.5.1)
   bio-genomic-interval (>= 0.1.2)
-  bundler (~> 1.3.5)
-  jeweler (~> 1.8.8)
+  bundler (>= 1.3.5)
+  jeweler (>= 2.3.7)
   mysql (~> 2.9.1)
-  rake (~> 10.1.0)
+  rake (>= 10.1.0)
   rdoc (>= 4.0.1)
-  rspec (~> 2.14.1)
+  rspec (>= 2.14.1)
   safe_attributes (~> 1.0.10)
+
+BUNDLED WITH
+   1.14.2

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2011-2013 MISHIMA, Hiroyuki
+Copyright (c) 2011-2017 MISHIMA, Hiroyuki
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -1,4 +1,4 @@
-# bio-ucsc-api version 0.6.2
+# bio-ucsc-api version 0.6.3
 
 **The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
 
@@ -18,6 +18,10 @@ http://www.biomedcentral.com/1471-2105/13/240/
 $ gem install bio-ucsc-api
 ```
 
+# Web Service
+
+TogoWS ( http://togows.org/ ), a web-service of DBCLS ( http://dbcls.rois.ac.jp/ ), supports UCSC Genome Database and offers the REST interface using the Ruby UCSC API internally. Please see the TogoWS API documentation (the "External API" section) at http://togows.org/help/ . 
+
 # Features
 
 * Supporting all organisms in the UCSC genome database.
@@ -33,7 +37,7 @@ $ gem install bio-ucsc-api
 
 # Supported databases (genome assemblies)
 
-If your favorite databese is not supported, please do not hesitate to contact the author. 
+If your favorite databese is not supported, please do not hesitate to contact the author because the author mainly working only with human genomes. 
 
 * **human** Hg38, Hg19, Hg18
 * **mammals** chimp (PanTro3), orangutan (PonAbe2), rhesus (RheMac2), marmoset (CalJac3), mouse (Mm10, Mm9), rat (Rn5, Rn4), guinea pig (CavPor3), rabbit (OryCun2), cat (FelCat4), panda (AilMel1), dog (CanFam2), horse (EquCab2), pig (SusScr2), sheep (OviAri1), cow (BosTau4), elephant (LoxAfr3), opossum (MonDom5), platypus (OrnAna1)
@@ -72,6 +76,7 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 # Change Log
+* **BUG-FIX** (v.0.6.3) Bio::Ucsc::File::TwoBit#find_by_interval fails in retrieving reference sequences including entire "N" blocks, e.g. "aaaNNttt".
 * **BUG-FIX** (v.0.6.2) NoMemoryError in Bio::Ucsc::File::Twobit.open. Now internally File.open is used instead of Kernel.open.  
 * **UPDATE** (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions. 
 * **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies. 
@@ -93,7 +98,6 @@ At first, you have to declare the API and establish the connection to a database
 
 ```ruby
  require 'bio-ucsc'
-
  DB = Bio::Ucsc::Hg19
  DB.connect
  
@@ -105,6 +109,7 @@ At first, you have to declare the API and establish the connection to a database
 Table search using genomic intervals:
 
 ```ruby
+ require 'bio-ucsc'
  DB = Bio::Ucsc::Hg19
  DB.connect
  
@@ -137,6 +142,7 @@ Table search using genomic intervals:
 Sometimes, queries using raw SQLs provide elegant solutions.
 
 ```ruby
+ require 'bio-ucsc'
  DB = Bio::Ucsc::Hg19
  DB.connect
  
@@ -150,6 +156,7 @@ Sometimes, queries using raw SQLs provide elegant solutions.
 For gene prediction (genePred) tables, such as RefSeq, EndGene, and WgEncodeGencodeBasicV12, Ruby UCSC API automatically implements `#exon`, `#introns`, `#cdss` (or an alias `#cdses`) methods. Exons, introns, and CDSes are accessible as Array objects of `Bio::GenomicInterval`.
 
 ```ruby
+ require 'bio-ucsc'
  DB = Bio::Ucsc::Hg19
  DB.connect
  
@@ -256,6 +263,6 @@ puts Bio::Ucsc::Hg19::Snp138.find_by_name("rs242").snp138Seq.first.file_offset
 ```
 
 # Copyright
-**Copyright**: (c) 2011-2014 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)  
+**Copyright**: (c) 2011-2017 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)  
 **Copyright**: (c) 2010 Jan Aerts  
 **License**: The MIT license. See LICENSE.txt for further details..

data/Rakefile

@@ -15,6 +15,7 @@ require 'jeweler'
 Jeweler::Tasks.new do |gem|
   # gem is a Gem::Specification...
   # see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.version = File.read('VERSION').chomp # <<<<<<<<<<<<<<<<<<<<<<<<<<<< manually added!
   gem.name = "bio-ucsc-api"
   gem.homepage = "http://github.com/misshie/bioruby-ucsc-api"
   gem.license = "The MIT License"

data/VERSION

@@ -1 +1 @@
-0.6.2
+0.6.3

data/bio-ucsc-api.gemspec

@@ -2,15 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-ucsc-api 0.6.2 ruby lib
+# stub: bio-ucsc-api 0.6.3 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-ucsc-api"
-  s.version = "0.6.2"
+  s.version = "0.6.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
   s.authors = ["Hiroyuki Mishima", "Jan Aerts"]
-  s.date = "2014-03-26"
+  s.date = "2017-08-17"
   s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
   s.email = "missy@be.to"
   s.extra_rdoc_files = [
@@ -265,8 +266,7 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/hg19/description.rb",
     "lib/bio-ucsc/hg19/gbcdnainfo.rb",
     "lib/bio-ucsc/hg38.rb",
-    "lib/bio-ucsc/hg38/description.rb",
-    "lib/bio-ucsc/hg38/gbcdnainfo.rb",
+    "lib/bio-ucsc/hg38/00README",
     "lib/bio-ucsc/hgfixed.rb",
     "lib/bio-ucsc/loxafr3.rb",
     "lib/bio-ucsc/mm10.rb",
@@ -439,8 +439,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/misshie/bioruby-ucsc-api"
   s.licenses = ["The MIT License"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "2.1.11"
+  s.rubygems_version = "2.5.1"
   s.summary = "The Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
 
   if s.respond_to? :specification_version then
@@ -453,11 +452,11 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<safe_attributes>, ["~> 1.0.10"])
       s.add_runtime_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
       s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-      s.add_development_dependency(%q<rake>, ["~> 10.1.0"])
-      s.add_development_dependency(%q<rspec>, ["~> 2.14.1"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.3.5"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.8.8"])
-      s.add_development_dependency(%q<bio>, [">= 1.4.3"])
+      s.add_development_dependency(%q<rake>, [">= 10.1.0"])
+      s.add_development_dependency(%q<rspec>, [">= 2.14.1"])
+      s.add_development_dependency(%q<bundler>, [">= 1.3.5"])
+      s.add_development_dependency(%q<jeweler>, [">= 2.3.7"])
+      s.add_development_dependency(%q<bio>, [">= 1.5.1"])
       s.add_development_dependency(%q<rdoc>, [">= 4.0.1"])
     else
       s.add_dependency(%q<activerecord>, ["~> 4.0.2"])
@@ -466,11 +465,11 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<safe_attributes>, ["~> 1.0.10"])
       s.add_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
       s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-      s.add_dependency(%q<rake>, ["~> 10.1.0"])
-      s.add_dependency(%q<rspec>, ["~> 2.14.1"])
-      s.add_dependency(%q<bundler>, ["~> 1.3.5"])
-      s.add_dependency(%q<jeweler>, ["~> 1.8.8"])
-      s.add_dependency(%q<bio>, [">= 1.4.3"])
+      s.add_dependency(%q<rake>, [">= 10.1.0"])
+      s.add_dependency(%q<rspec>, [">= 2.14.1"])
+      s.add_dependency(%q<bundler>, [">= 1.3.5"])
+      s.add_dependency(%q<jeweler>, [">= 2.3.7"])
+      s.add_dependency(%q<bio>, [">= 1.5.1"])
       s.add_dependency(%q<rdoc>, [">= 4.0.1"])
     end
   else
@@ -480,11 +479,11 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<safe_attributes>, ["~> 1.0.10"])
     s.add_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
     s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-    s.add_dependency(%q<rake>, ["~> 10.1.0"])
-    s.add_dependency(%q<rspec>, ["~> 2.14.1"])
-    s.add_dependency(%q<bundler>, ["~> 1.3.5"])
-    s.add_dependency(%q<jeweler>, ["~> 1.8.8"])
-    s.add_dependency(%q<bio>, [">= 1.4.3"])
+    s.add_dependency(%q<rake>, [">= 10.1.0"])
+    s.add_dependency(%q<rspec>, [">= 2.14.1"])
+    s.add_dependency(%q<bundler>, [">= 1.3.5"])
+    s.add_dependency(%q<jeweler>, [">= 2.3.7"])
+    s.add_dependency(%q<bio>, [">= 1.5.1"])
     s.add_dependency(%q<rdoc>, [">= 4.0.1"])
   end
 end

data/lib/bio-ucsc-api.rb

@@ -1,8 +1,8 @@
 #
 # = bio-ucsc-api.rb
-# Copyright::   Cioyrught (C) 2011
+# Copyright::   Cioyrught (C) 2011-2017
 #               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     Ruby licence (Ryby's / GPLv2 dual)
+# License::     The MIT license
 #
 # Just a alias for bio-ucsc
 

data/lib/bio-ucsc.rb

@@ -1,8 +1,8 @@
 #
 # = bio-ucsc.rb
-# Copyright::   Copyright (C) 2011-2013
+# Copyright::   Copyright (C) 2011-2017
 #               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     Ruby licence (Ryby's / GPLv2 dual)
+# License::     The MIT license
 
 base = "#{::File.dirname(__FILE__)}/bio-ucsc"
 
@@ -21,7 +21,7 @@ require "#{base}/gi.rb"
 
 module Bio
   module Ucsc
-    VERSION = "0.6.1"
+    VERSION = "0.6.3"
     base = "#{::File.dirname(__FILE__)}/bio-ucsc"
     
     # mammmals #####################################

data/lib/bio-ucsc/file/twobit.rb

@@ -2,7 +2,7 @@
 # = twobit.rb
 # handle UCSC's 2bit file (locally stored) to retrieve the reference sequence
 #
-# Copyright::   Copyright (C) 2011, 2012, 2014
+# Copyright::   Copyright (C) 2011, 2012, 2014, 2017
 #               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The MIT license
 
@@ -122,12 +122,25 @@ module Bio
               when :equal,:contains
                 seq = 'N' * interval.overlap(nb)
               when :contained_by
-                left_len  = nb.chr_start - interval.chr_start + 1           
-                right_len = interval.chr_end - nb.chr_end + 1                
-                seq =
-                  seq[0 .. left_len] +
-                  'N' * (seq.length - left_len - right_len) +
-                  seq[-right_len ..  -1]
+                left_len  = nb.chr_start - interval.chr_start           
+                right_len = interval.chr_end - nb.chr_end
+                case
+                when left_len > 0 && right_len > 0
+                  seq =
+                    seq[0 .. (left_len-1)] +
+                    'N' * (seq.length - left_len - right_len) +
+                    seq[-right_len ..  -1]
+                when left_len == 0 && right_len > 0
+                  seq =
+                    'N' * (seq.length - left_len - right_len) +
+                    seq[-right_len ..  -1]
+                when left_len > 0 && right_len == 0
+                  seq =
+                    seq[0 .. (left_len-1)] +
+                    'N' * (seq.length - left_len - right_len)
+                else
+                  raise "This should not happen! (Bio::Ucsc::File::Twobit#find_by_interval)"
+                end
               when :left_overlapped
                 left_len = nb.chr_end - interval.chr_start + 1
                 seq[0, left_len] = 'N' * left_len

data/lib/bio-ucsc/hg38/00README

@@ -0,0 +1 @@
+description.rb and gbcddnainfo.rb are removed because they are already not exit on UCSC's MySQL.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.6.2
+  version: 0.6.3
 platform: ruby
 authors:
 - Hiroyuki Mishima
@@ -9,179 +9,177 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-26 00:00:00.000000000 Z
+date: 2017-08-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 4.0.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 4.0.2
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 4.0.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 4.0.2
 - !ruby/object:Gem::Dependency
   name: mysql
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.9.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.9.1
 - !ruby/object:Gem::Dependency
   name: safe_attributes
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.10
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.10
 - !ruby/object:Gem::Dependency
   name: activerecord-deprecated_finders
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.0.3
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 10.1.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 10.1.0
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.14.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.14.1
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.5
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.5
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.8.8
+        version: 2.3.7
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.8.8
+        version: 2.3.7
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MS40LjM=
+        version: 1.5.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MS40LjM=
+        version: 1.5.1
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.1
-description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
+description: 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
 extensions: []
@@ -436,8 +434,7 @@ files:
 - lib/bio-ucsc/hg19/description.rb
 - lib/bio-ucsc/hg19/gbcdnainfo.rb
 - lib/bio-ucsc/hg38.rb
-- lib/bio-ucsc/hg38/description.rb
-- lib/bio-ucsc/hg38/gbcdnainfo.rb
+- lib/bio-ucsc/hg38/00README
 - lib/bio-ucsc/hgfixed.rb
 - lib/bio-ucsc/loxafr3.rb
 - lib/bio-ucsc/mm10.rb
@@ -617,18 +614,18 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.11
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
-summary: ! 'The Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
+summary: 'The Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 test_files: []

data/lib/bio-ucsc/hg38/description.rb

@@ -1,16 +0,0 @@
-#
-# Hg19::Description has "id" colomn that is primary key
-#
-
-module Bio
-  module Ucsc
-    module Hg38
-      class Description < DBConnection
-        self.table_name = "description"
-        self.inheritance_column = nil
-      end
-    end
-  end
-end
-
-        

data/lib/bio-ucsc/hg38/gbcdnainfo.rb

@@ -1,14 +0,0 @@
-#
-# Hg19::GbCdnaInfo has "id" colomn that is primary key
-#
-
-module Bio
-  module Ucsc
-    module Hg38
-      class GbCdnaInfo < DBConnection
-        self.table_name = "gbCdnaInfo"
-        self.inheritance_column = nil
-      end
-    end
-  end
-end