bio-ucsc-api 0.0.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color
+--format documentation

data/COPYING

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+BioRuby is copyrighted free software by
+  Hiroyuki Mishima <missy at be.to> / <hmishima at nagasaki-u.ac.jp>, and
+  Jan Aerts <jan.aerts@gmail.com>.
+You can redistribute it and/or modify it under either the terms of the GPL
+version 2 (see the file GPL), or the conditions below:
+
+  1. You may make and give away verbatim copies of the source form of the
+     software without restriction, provided that you duplicate all of the
+     original copyright notices and associated disclaimers.
+
+  2. You may modify your copy of the software in any way, provided that
+     you do at least ONE of the following:
+
+       a) place your modifications in the Public Domain or otherwise
+          make them Freely Available, such as by posting said
+	  modifications to Usenet or an equivalent medium, or by allowing
+	  the author to include your modifications in the software.
+
+       b) use the modified software only within your corporation or
+          organization.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  3. You may distribute the software in object code or binary form,
+     provided that you do at least ONE of the following:
+
+       a) distribute the binaries and library files of the software,
+	  together with instructions (in the manual page or equivalent)
+	  on where to get the original distribution.
+
+       b) accompany the distribution with the machine-readable source of
+	  the software.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  4. You may modify and include the part of the software into any other
+     software (possibly commercial).  But some files in the distribution
+     are not written by the author, so that they are not under these terms.
+
+     For the list of those files and their copying conditions, see the
+     file LEGAL.
+
+  5. The scripts and library files supplied as input to or produced as 
+     output from the software do not automatically fall under the
+     copyright of the software, but belong to whomever generated them, 
+     and may be sold commercially, and may be aggregated with this
+     software.
+
+  6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+     IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+     PURPOSE.

data/COPYING.ja

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data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "activerecord",         ">= 3.0.7"
+#gem "activesupport",        ">= 3.0.0"
+gem "mysql",                ">= 2.8.1"
+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 "rspec", "~> 2.5.0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+#  gem "cover_me", ">= 1.0.0.rc6"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    activemodel (3.0.7)
+      activesupport (= 3.0.7)
+      builder (~> 2.1.2)
+      i18n (~> 0.5.0)
+    activerecord (3.0.7)
+      activemodel (= 3.0.7)
+      activesupport (= 3.0.7)
+      arel (~> 2.0.2)
+      tzinfo (~> 0.3.23)
+    activesupport (3.0.7)
+    arel (2.0.9)
+    bio (1.4.1)
+    bio-genomic-interval (0.1.2)
+    builder (2.1.2)
+    diff-lcs (1.1.2)
+    git (1.2.5)
+    i18n (0.5.0)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    mysql (2.8.1)
+    rake (0.8.7)
+    rcov (0.9.9)
+    rspec (2.5.0)
+      rspec-core (~> 2.5.0)
+      rspec-expectations (~> 2.5.0)
+      rspec-mocks (~> 2.5.0)
+    rspec-core (2.5.1)
+    rspec-expectations (2.5.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.5.0)
+    tzinfo (0.3.26)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  activerecord (>= 3.0.7)
+  bio (>= 1.4.1)
+  bio-genomic-interval (>= 0.1.2)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.2)
+  mysql (>= 2.8.1)
+  rcov
+  rspec (~> 2.5.0)

data/README.rdoc

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+= bio-ucsc-api
+
+A BioRuby plugin: Ruby API for the UCSC database.
+
+This package is based on the followings:
+* ruby-ucsc-api: https://github.com/jandot/ruby-ucsc-api
+* ruby-ensembl-api: https://github.com/jandot/ruby-ensembl-api
+
+Major dependent gems:
+* active_record http://api.rubyonrails.org/classes/ActiveRecord/Base.html
+* bioruby-genomic-interval https://github.com/misshie/bioruby-genomic-interval
+
+See also a paper:
+
+Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features.
+Bioinformatics 2011, 27:1013-1014.
+
+NOTE: THIS PACKAGE IS STILL VERY PRELIMINARY VERSION. 
+Your comments, suggestions and requests are welcome.
+Email to the author (missy at be.to) or create an "Issue" at
+http://github.com/misshie/bioruby-ucsc-api/issues
+
+== Features
+
+* Designed as a BioRuby plugin
+* Using the Bin index system to improve query performance (see https://github.com/misshie/UCSCBin )
+* Automatic conversion of "1-based full-closed intervals" to internal "0-based half-closed intervals" (see also bioruby-genomic-interval)
+* Supporting non-official MySql hosts (e.g. local servers)
+* Using Rspec for the testing framework
+* Trying to support whole hg19 and hg18 databases.
+
+
+== Install
+
+ (to be uploaded into rubygems.org)
+
+== How to Use
+
+ requre 'bio-ucsc'
+
+ Bio::Ucsc::Hg19::DBConnection.connect
+
+ itv =  Bio::GenomicInterval.parse("chr1:1-11,000")
+ Bio::Ucsc::Hg19::Snp131.find_by_interval(itv).each do |e|
+   i = Bio::GenomicInterval.zero_based(e.chrom, e.chromStart, e.chromEnd)
+   puts "#{i.chrom}\t#{i.chromStart}\t#{e.name}\t#{e[:class]}"
+ end
+
+ p Bio::Ucsc::Hg19::Snp131.find_by_name("rs56289060")
+
+== Copyright
+Copyright:: (c) 2011 MISHIMA, Hiroyuki (missy at be.to / hmishima at nagasaki-u.ac.jp)
+
+Copyright:: (c) 2008-2011 Francesco Strozzi, Jan Aerts
+
+License:: Ruby licence (Ruby's / GPLv2 dual). See COPYING and COPYING.ja for further details.
+

data/Rakefile

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification...
+  # see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-ucsc-api"
+  gem.homepage = "http://github.com/misshie/bioruby-ucsc-api"
+  gem.license = "Ruby (Ruby's/GPLv2 dual)"
+  gem.summary = %Q{A Bioruby plugin: an API for UCSC Genome Browser (experimental)}
+  gem.description = %Q{A Bioruby plugin: an API for UCSC Genome Browser (experimental)}
+  gem.email = "missy@be.to"
+  gem.authors = ["MISHIMA, Hiroyuki", "Francesco Strozzi", "Jan Aerts"]
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development
+  # (ie running rake tasks, tests, etc)
+  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
+  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+
+  gem.add_runtime_dependency 'activerecord',         '>= 3.0.0'
+  gem.add_runtime_dependency 'activesupport',        '>= 3.0.0'
+  gem.add_runtime_dependency 'bio-genomic-interval', '>= 0.1.1'
+end
+
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :default => :spec
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-ucsc-api #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+# namespace :cover_me do
+#   task :report do
+#     require 'cover_me'
+#     CoverMe.complete!
+#   end
+# end
+
+# task :test do
+#   Rake::Task['cover_me:report'].invoke
+# end
+
+# task :spec do
+#   Rake::Task['cover_me:report'].invoke
+# end

data/VERSION

@@ -0,0 +1 @@
+0.0.1

data/bio-ucsc-api.gemspec

@@ -0,0 +1,212 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{bio-ucsc-api}
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["MISHIMA, Hiroyuki", "Francesco Strozzi", "Jan Aerts"]
+  s.date = %q{2011-04-22}
+  s.description = %q{A Bioruby plugin: an API for UCSC Genome Browser (experimental)}
+  s.email = %q{missy@be.to}
+  s.extra_rdoc_files = [
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    "COPYING",
+    "COPYING.ja",
+    "Gemfile",
+    "Gemfile.lock",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-ucsc-api.gemspec",
+    "lib/bio-ucsc.rb",
+    "lib/bio-ucsc/hg18.rb",
+    "lib/bio-ucsc/hg18/activerecord.rb",
+    "lib/bio-ucsc/hg18/cnpiafrate2.rb",
+    "lib/bio-ucsc/hg18/cnplocke.rb",
+    "lib/bio-ucsc/hg18/cnpredon.rb",
+    "lib/bio-ucsc/hg18/cnpsebat2.rb",
+    "lib/bio-ucsc/hg18/cnpsharp2.rb",
+    "lib/bio-ucsc/hg18/db_connection.rb",
+    "lib/bio-ucsc/hg18/dgv.rb",
+    "lib/bio-ucsc/hg18/refgene.rb",
+    "lib/bio-ucsc/hg18/rmsk.rb",
+    "lib/bio-ucsc/hg18/tables.rb",
+    "lib/bio-ucsc/hg19.rb",
+    "lib/bio-ucsc/hg19/activerecord.rb",
+    "lib/bio-ucsc/hg19/ccdsgene.rb",
+    "lib/bio-ucsc/hg19/cytoband.rb",
+    "lib/bio-ucsc/hg19/db_connection.rb",
+    "lib/bio-ucsc/hg19/dgv.rb",
+    "lib/bio-ucsc/hg19/ensgene.rb",
+    "lib/bio-ucsc/hg19/gwascatalog.rb",
+    "lib/bio-ucsc/hg19/hapmapalleleschimp.rb",
+    "lib/bio-ucsc/hg19/hapmapallelesmacaque.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpsasw.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpsceu.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpschb.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpschd.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpsgih.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpsjpt.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpslwk.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpsmex.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpsmkk.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpstsi.rb",
+    "lib/bio-ucsc/hg19/hapmapsnpsyri.rb",
+    "lib/bio-ucsc/hg19/knowngene.rb",
+    "lib/bio-ucsc/hg19/omimgene.rb",
+    "lib/bio-ucsc/hg19/phastconselements46wayprimates.rb",
+    "lib/bio-ucsc/hg19/phylop46wayprimates.rb",
+    "lib/bio-ucsc/hg19/refgene.rb",
+    "lib/bio-ucsc/hg19/rmsk.rb",
+    "lib/bio-ucsc/hg19/snp131.rb",
+    "lib/bio-ucsc/hg19/snp132.rb",
+    "lib/bio-ucsc/hg19/snp132codingdbsnp.rb",
+    "lib/bio-ucsc/hg19/snp132common.rb",
+    "lib/bio-ucsc/hg19/snp132flagged.rb",
+    "lib/bio-ucsc/hg19/snp132mult.rb",
+    "lib/bio-ucsc/hg19/wgrna.rb",
+    "lib/bio-ucsc/ucsc_bin.rb",
+    "samples/hg19-sample.rb",
+    "spec/hg18/cnpiafrate2_spec.rb",
+    "spec/hg18/cnplocke_spec.rb",
+    "spec/hg18/cnpredon_spec.rb",
+    "spec/hg18/cnpsebat2_spec.rb",
+    "spec/hg18/cnpsharp2_spec.rb",
+    "spec/hg18/db_connection_spec.rb",
+    "spec/hg18/dgv_spec.rb",
+    "spec/hg18/refgene_spec.rb",
+    "spec/hg18/rmsk_spec.rb",
+    "spec/hg19/ccdsgene_spec.rb",
+    "spec/hg19/cytoband_spec.rb",
+    "spec/hg19/db_connection_spec.rb",
+    "spec/hg19/dgv_spec.rb",
+    "spec/hg19/ensgene_spec.rb",
+    "spec/hg19/gwascatalog_spec.rb",
+    "spec/hg19/hapmapalleleschimp_spec.rb",
+    "spec/hg19/hapmapallelesmacaque_spec.rb",
+    "spec/hg19/hapmapsnpsasw_spec.rb",
+    "spec/hg19/hapmapsnpsceu_spec.rb",
+    "spec/hg19/hapmapsnpschb_spec.rb",
+    "spec/hg19/hapmapsnpschd_spec.rb",
+    "spec/hg19/hapmapsnpsgih_spec.rb",
+    "spec/hg19/hapmapsnpsjpt_spec.rb",
+    "spec/hg19/hapmapsnpslwk_spec.rb",
+    "spec/hg19/hapmapsnpsmex_spec.rb",
+    "spec/hg19/hapmapsnpsmkk_spec.rb",
+    "spec/hg19/hapmapsnpstsi_spec.rb",
+    "spec/hg19/hapmapsnpsyri_spec.rb",
+    "spec/hg19/knowngene_spec.rb",
+    "spec/hg19/omimGene_spec.rb",
+    "spec/hg19/phastconselements46wayprimates_spec.rb",
+    "spec/hg19/phyloP46wayPrimates_spec.rb",
+    "spec/hg19/refgene_spec.rb",
+    "spec/hg19/rmsk_spec.rb",
+    "spec/hg19/snp132Flagged_spec.rb",
+    "spec/hg19/snp132_spec.rb",
+    "spec/hg19/snp132codingdbsnp_spec.rb",
+    "spec/hg19/snp132common_spec.rb",
+    "spec/hg19/snp132mult_spec.rb",
+    "spec/hg19/wgrna_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = %q{http://github.com/misshie/bioruby-ucsc-api}
+  s.licenses = ["Ruby (Ruby's/GPLv2 dual)"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{A Bioruby plugin: an API for UCSC Genome Browser (experimental)}
+  s.test_files = [
+    "spec/hg18/cnpiafrate2_spec.rb",
+    "spec/hg18/cnplocke_spec.rb",
+    "spec/hg18/cnpredon_spec.rb",
+    "spec/hg18/cnpsebat2_spec.rb",
+    "spec/hg18/cnpsharp2_spec.rb",
+    "spec/hg18/db_connection_spec.rb",
+    "spec/hg18/dgv_spec.rb",
+    "spec/hg18/refgene_spec.rb",
+    "spec/hg18/rmsk_spec.rb",
+    "spec/hg19/ccdsgene_spec.rb",
+    "spec/hg19/cytoband_spec.rb",
+    "spec/hg19/db_connection_spec.rb",
+    "spec/hg19/dgv_spec.rb",
+    "spec/hg19/ensgene_spec.rb",
+    "spec/hg19/gwascatalog_spec.rb",
+    "spec/hg19/hapmapalleleschimp_spec.rb",
+    "spec/hg19/hapmapallelesmacaque_spec.rb",
+    "spec/hg19/hapmapsnpsasw_spec.rb",
+    "spec/hg19/hapmapsnpsceu_spec.rb",
+    "spec/hg19/hapmapsnpschb_spec.rb",
+    "spec/hg19/hapmapsnpschd_spec.rb",
+    "spec/hg19/hapmapsnpsgih_spec.rb",
+    "spec/hg19/hapmapsnpsjpt_spec.rb",
+    "spec/hg19/hapmapsnpslwk_spec.rb",
+    "spec/hg19/hapmapsnpsmex_spec.rb",
+    "spec/hg19/hapmapsnpsmkk_spec.rb",
+    "spec/hg19/hapmapsnpstsi_spec.rb",
+    "spec/hg19/hapmapsnpsyri_spec.rb",
+    "spec/hg19/knowngene_spec.rb",
+    "spec/hg19/omimGene_spec.rb",
+    "spec/hg19/phastconselements46wayprimates_spec.rb",
+    "spec/hg19/phyloP46wayPrimates_spec.rb",
+    "spec/hg19/refgene_spec.rb",
+    "spec/hg19/rmsk_spec.rb",
+    "spec/hg19/snp132Flagged_spec.rb",
+    "spec/hg19/snp132_spec.rb",
+    "spec/hg19/snp132codingdbsnp_spec.rb",
+    "spec/hg19/snp132common_spec.rb",
+    "spec/hg19/snp132mult_spec.rb",
+    "spec/hg19/wgrna_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<activerecord>, [">= 3.0.7"])
+      s.add_runtime_dependency(%q<mysql>, [">= 2.8.1"])
+      s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.5.0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_runtime_dependency(%q<activerecord>, [">= 3.0.0"])
+      s.add_runtime_dependency(%q<activesupport>, [">= 3.0.0"])
+      s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.1"])
+    else
+      s.add_dependency(%q<activerecord>, [">= 3.0.7"])
+      s.add_dependency(%q<mysql>, [">= 2.8.1"])
+      s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
+      s.add_dependency(%q<rspec>, ["~> 2.5.0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<activerecord>, [">= 3.0.0"])
+      s.add_dependency(%q<activesupport>, [">= 3.0.0"])
+      s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.1"])
+    end
+  else
+    s.add_dependency(%q<activerecord>, [">= 3.0.7"])
+    s.add_dependency(%q<mysql>, [">= 2.8.1"])
+    s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
+    s.add_dependency(%q<rspec>, ["~> 2.5.0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<activerecord>, [">= 3.0.0"])
+    s.add_dependency(%q<activesupport>, [">= 3.0.0"])
+    s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.1"])
+  end
+end
+