bio-ucsc-api 0.6.4 → 0.6.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/ChangeLog.md

@@ -1,4 +1,6 @@
 #Change Log
+ * **UPDATE** (v.0.6.5) Support Zebrafish DanRer10 and DanRer11 references.
+ * **UPDATE** (v.0.6.4) Support Ruby 2.4 by using Rails 4.2 and the MySql2 gem v0.4 at BioHackathon2017 http://20
  * **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.

data/Gemfile.lock

@@ -48,14 +48,14 @@ GEM
       semver2
     jwt (1.5.6)
     mime-types (2.99.3)
-    mini_portile2 (2.2.0)
+    mini_portile2 (2.3.0)
     minitest (5.10.3)
     multi_json (1.12.2)
     multi_xml (0.6.0)
     multipart-post (2.0.0)
     mysql2 (0.4.9)
-    nokogiri (1.8.0)
-      mini_portile2 (~> 2.2.0)
+    nokogiri (1.8.2)
+      mini_portile2 (~> 2.3.0)
     oauth2 (1.4.0)
       faraday (>= 0.8, < 0.13)
       jwt (~> 1.0)

data/README.md

@@ -1,4 +1,4 @@
-# bio-ucsc-api version 0.6.4
+# bio-ucsc-api version 0.6.5 [![Build Status](https://travis-ci.org/misshie/bioruby-ucsc-api.svg?branch=master)](https://travis-ci.org/misshie/bioruby-ucsc.api)
 
 **The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
 
@@ -41,7 +41,7 @@ If your favorite databese is not supported, please do not hesitate to contact th
 
 * **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)
-* **vertebrates** chicken (GalGal3), zebra finch (TaeGut1), lizard (AnoCar2), X. tropicalis (XenTro2), zebrafish (DanRer7), tetraodon (TetNig2), fugu (Fr2), stickleback (GasAcu1), medaka (OryLat2), lamprey (PetMar1)
+* **vertebrates** chicken (GalGal3), zebra finch (TaeGut1), lizard (AnoCar2), X. tropicalis (XenTro2), zebrafish (DanRer7, DanRer10, DanRer11), tetraodon (TetNig2), fugu (Fr2), stickleback (GasAcu1), medaka (OryLat2), lamprey (PetMar1)
 * **deuterostomes** lancelet (BraFlo1), sea squirt (Ci2), sea urchin (StrPur2)
 [insects] D.melanogaster (Dm3), D.simulans (DroSim1), D.sechellia (DroSec1), D.yakuba (DroYak2), D.erecta (DroEre1), D.ananassae (DroAna2), D.pseudoobscura (Dp3), D.persimilis (DroPer1), D.virilis (DroVir2), D.mojavensis (DroMoj2), D.grimshawi (DroGri1), Anopheles mosquito (AnoGam1), honey bee (ApiMel2)
 * **nematodes** C.elegans (Ce6), C.brenneri (CaePb3), C.briggsae (Cb3), C.remanei (CaeRem3), C.japonica (CaeJap1), P.pacificus (PriPac1)
@@ -76,8 +76,9 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 # Change Log
-* **UPDATE** (v.0.6.4) Supporting Ruby 2.4 by using Rails 4.2 and the MySql2 gem v0.4 at BioHackathon2017 http://2017.biohackathon.org .
-* **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".
+* **UPDATE** (v.0.6.5) Support Zebrafish DanRer10 and DanRer11 references.
+* **UPDATE** (v.0.6.4) Support Ruby 2.4 by using Rails 4.2 and the MySql2 gem v0.4 at BioHackathon2017 http://2017.biohackathon.org .
+* **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", "gggNccc", etc. .
 * **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. 
@@ -264,6 +265,6 @@ puts Bio::Ucsc::Hg19::Snp138.find_by_name("rs242").snp138Seq.first.file_offset
 ```
 
 # Copyright
-**Copyright**: (c) 2011-2017 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)  
+**Copyright**: (c) 2011-2018 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

@@ -15,7 +15,8 @@ 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.version = File.read('VERSION').chomp # manually added
+  gem.required_ruby_version = '>= 1.9.3'   # 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 @@
-0.6.4
+0.6.5

data/bio-ucsc-api.gemspec

@@ -2,16 +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 0.6.4 ruby lib
+# stub: bio-ucsc-api 0.6.5 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-ucsc-api".freeze
-  s.version = "0.6.4"
+  s.version = "0.6.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Hiroyuki Mishima".freeze, "Jan Aerts".freeze]
-  s.date = "2017-09-12"
+  s.date = "2018-05-11"
   s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby".freeze
   s.email = "missy@be.to".freeze
   s.extra_rdoc_files = [
@@ -125,6 +125,8 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/ce6/rmsk.rb",
     "lib/bio-ucsc/ce6/t25mersrepeats.rb",
     "lib/bio-ucsc/ci2.rb",
+    "lib/bio-ucsc/danrer10.rb",
+    "lib/bio-ucsc/danrer11.rb",
     "lib/bio-ucsc/danrer7.rb",
     "lib/bio-ucsc/dm3.rb",
     "lib/bio-ucsc/dm3/chainanogam1.rb",
@@ -439,6 +441,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/misshie/bioruby-ucsc-api".freeze
   s.licenses = ["The MIT License".freeze]
+  s.required_ruby_version = Gem::Requirement.new(">= 1.9.3".freeze)
   s.rubygems_version = "2.6.11".freeze
   s.summary = "The Ruby UCSC API: accessing the UCSC Genome Database using Ruby".freeze
 

data/lib/bio-ucsc.rb

@@ -98,7 +98,9 @@ module Bio
     autoload :XenTro2, "#{base}/xentro2"
 
     # zebrafish genome assemblies
-    autoload :DanRer7, "#{base}/danrer7"
+    autoload :DanRer7,  "#{base}/danrer7"
+    autoload :DanRer10, "#{base}/danrer10"
+    autoload :DanRer11, "#{base}/danrer11"
 
     # tetraodon genome assemblies
     autoload :TetNig2, "#{base}/tetnig2"

data/lib/bio-ucsc/danrer10.rb

@@ -0,0 +1,65 @@
+#
+# = AUTOMATIC Table Definition of the Zebrafish Jul. 2010 (GRCz10/danRer10) assembly
+# Copyright::   Copyright (C) 2011-2018
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The MIT licence
+#
+
+require "#{::File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module DanRer10
+      CHROMS = 
+%w(Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10
+Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 
+Chr20 Chr21 Chr22 Chr23 Chr24 Chr25)
+
+      extend TableClassDetector
+      def self.default
+        DBConnection.default
+      end
+
+      def self.connect(param = Hash.new)
+        DBConnection.db_adapter = param[:db_adapter] if param[:db_adapter]
+        DBConnection.db_host = param[:db_host] if param[:db_host]
+        DBConnection.db_username = param[:db_username] if param[:db_username]
+        DBConnection.password = param[:password] if param[:password]
+        DBConnection.connect
+      end
+
+      class DBConnection < ActiveRecord::Base
+        include SafeAttributes
+        self.inheritance_column = 'dummy_not_to_use'
+
+        @@db_adapter  ||= 'mysql2'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+        @@db_name     ||= 'danRer10'
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql2'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => @@db_name,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end # class DBConnection
+
+      base = "#{::File.dirname(__FILE__)}/danrer10"
+    end
+  end
+end

data/lib/bio-ucsc/danrer11.rb

@@ -0,0 +1,65 @@
+#
+# = AUTOMATIC Table Definition of the Zebrafish Jul. 2010 (GRCz11/danRer11) assembly
+# Copyright::   Copyright (C) 2011-2018
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The MIT licence
+#
+
+require "#{::File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module DanRer11
+      CHROMS = 
+%w(Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10
+Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 
+Chr20 Chr21 Chr22 Chr23 Chr24 Chr25)
+
+      extend TableClassDetector
+      def self.default
+        DBConnection.default
+      end
+
+      def self.connect(param = Hash.new)
+        DBConnection.db_adapter = param[:db_adapter] if param[:db_adapter]
+        DBConnection.db_host = param[:db_host] if param[:db_host]
+        DBConnection.db_username = param[:db_username] if param[:db_username]
+        DBConnection.password = param[:password] if param[:password]
+        DBConnection.connect
+      end
+
+      class DBConnection < ActiveRecord::Base
+        include SafeAttributes
+        self.inheritance_column = 'dummy_not_to_use'
+
+        @@db_adapter  ||= 'mysql2'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+        @@db_name     ||= 'danRer11'
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql2'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => @@db_name,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end # class DBConnection
+
+      base = "#{::File.dirname(__FILE__)}/danrer10"
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.6.4
+  version: 0.6.5
 platform: ruby
 authors:
 - Hiroyuki Mishima
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-09-12 00:00:00.000000000 Z
+date: 2018-05-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
@@ -293,6 +293,8 @@ files:
 - lib/bio-ucsc/ce6/rmsk.rb
 - lib/bio-ucsc/ce6/t25mersrepeats.rb
 - lib/bio-ucsc/ci2.rb
+- lib/bio-ucsc/danrer10.rb
+- lib/bio-ucsc/danrer11.rb
 - lib/bio-ucsc/danrer7.rb
 - lib/bio-ucsc/dm3.rb
 - lib/bio-ucsc/dm3/chainanogam1.rb
@@ -616,7 +618,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.9.3
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="