bio-ensembl 1.1.0

data/.document

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

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 "bio", ">= 1.4.1"
+gem "mysql"
+gem "activerecord", "= 3.0.0"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+  gem "mysql"
+  gem 'activerecord', "= 3.0.0"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    activemodel (3.0.0)
+      activesupport (= 3.0.0)
+      builder (~> 2.1.2)
+      i18n (~> 0.4.1)
+    activerecord (3.0.0)
+      activemodel (= 3.0.0)
+      activesupport (= 3.0.0)
+      arel (~> 1.0.0)
+      tzinfo (~> 0.3.23)
+    activesupport (3.0.0)
+    arel (1.0.1)
+      activesupport (~> 3.0.0)
+    bio (1.4.2)
+    builder (2.1.2)
+    git (1.2.5)
+    i18n (0.4.2)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    mysql (2.8.1)
+    rake (0.9.2.2)
+    rcov (0.9.11)
+    shoulda (2.11.3)
+    tzinfo (0.3.31)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  activerecord (= 3.0.0)
+  bio (>= 1.4.1)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.2)
+  mysql
+  rcov
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2011 Jan Aerts and Francesco Strozzi
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= bio-ensembl
+
+Ruby API to access the Ensembl database
+
+== Contributing to bio-ensembl
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 Jan Aerts and Francesco Strozzi. See LICENSE.txt 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-ensembl"
+  gem.homepage = "http://github.com/fstrozzi/bioruby-ensembl"
+  gem.license = "MIT"
+  gem.summary = "A Ruby API to the Ensembl database"
+  gem.description = "This API provides a complete set of methods and classes to access the Ensembl database using Ruby programming language"
+  gem.email = ["jan.aerts@gmail.com","francesco.strozzi@gmail.com"]
+  gem.authors = ["Jan Aerts","Francesco Strozzi"]
+  # 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)
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+# Tests
+
+namespace :test do
+  desc "Run tests for last supported release"
+  task :last => :default do
+    name = Dir.glob("test/release_*").sort[-1]
+    Dir.glob(name+"/**/*test_*.rb").each do |test_case|
+      ruby test_case
+    end
+  end
+  
+  desc "Run all tests"
+  task :all => :default do
+    Dir.glob("test//test_*.rb").each do |test_case|
+      ruby test_case
+    end
+  end
+  
+  desc "Run default tests"
+  task :default do
+    Dir.glob("test/default/test_*.rb").each do |test_case|
+      ruby test_case
+    end
+  end
+
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-ensembl #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+1.1.0

data/bin/ensembl

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+#!/usr/bin/ruby
+require 'irb'
+require File.expand_path File.join(File.dirname(__FILE__),'../lib/bio-ensembl')
+
+module IRB
+  def self.start_session(binding)
+    IRB.setup(nil)
+
+    workspace = WorkSpace.new(binding)
+
+    if @CONF[:SCRIPT]
+      irb = Irb.new(workspace, @CONF[:SCRIPT])
+    else
+      irb = Irb.new(workspace)
+    end
+
+    @CONF[:IRB_RC].call(irb.context) if @CONF[:IRB_RC]
+    @CONF[:MAIN_CONTEXT] = irb.context
+
+    trap("SIGINT") do
+      irb.signal_handle
+    end
+
+    catch(:IRB_EXIT) do
+      irb.eval_input
+    end
+  end
+end
+
+include Ensembl::Core
+include Ensembl::Variation
+if ARGV.length == 2
+  species = ARGV.shift
+  release = ARGV.shift.to_i
+  Ensembl::Core::DBConnection.connect(species,release)
+  Ensembl::Variation::DBConnection.connect(species,release)
+  IRB.start_session(Kernel.binding)
+else
+  raise "ERROR: Please provide snake_case species and Ensembl release number"
+end

data/bin/variation_effect_predictor

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+#!/usr/bin/env ruby
+
+def run_calculations(args)
+  
+  ### GETTING COMMAND LINE PARAMETERS ###
+  args.each_index {|x| args.insert(x+1,1) if args[x] == '-h' or args[x] == '-g' } # to have always an even number of parameters
+  params = Hash[*args]
+
+  ### PRINT HELP ###
+  if params.key?("-h") then
+    show_help()
+    exit
+  end
+
+  ### CHECKING INPUT FILE ###
+  if params["-i"].nil? or params == {} then
+    show_help()
+    puts "\nERROR: You must provide an input file!\n\n"
+    exit
+  end
+
+  ### SETTING DEFAULT MySQL USER IF NOT SPECIFIED ###
+  params["-u"] = "anonymous" if params["-u"].nil?
+  params["-P"] = params["-P"].to_i if params["-P"] != nil
+
+  ### OPENING CONNECTION TO ENSEMBL DATABASE ###
+  require 'rubygems'
+  require 'bio-ensembl'
+  include Ensembl::Variation
+
+  if params.key?("-g") then
+    params["-d"] = "mysql.ebi.ac.uk" if params["-d"].nil?
+    if params["-s"].nil? or params["-r"].nil? then
+      puts "\nERROR: For Ensembl Genomes you must provide a valid species and release number!\n\n"
+      exit
+    end
+    DBConnection.ensemblgenomes_connect(params["-s"],params["-r"].to_i,:host => params["-d"], :username => params["-u"],:password => params["-p"],:port => params["-P"])
+  else
+    params["-s"] = "homo_sapiens" if params["-s"].nil?
+    params["-r"] = 60 if params["-r"].nil?
+    params["-d"] = "ensembldb.ensembl.org" if params["-d"].nil?
+    DBConnection.connect(params["-s"],params["-r"].to_i,:host => params["-d"], :username => params["-u"],:password => params["-p"],:port => params["-P"])
+  end
+
+  ### STARTING VARIATIONS PREDICTIONS ###
+  File.open(params["-i"]) do |f|
+    f.each_line do |l|
+      next if l =~ /^#/
+      l.chomp!
+      data = l.split("\t")
+      get_consequence(data[0],data[1],data[2],data[3],data[4],data[5]).each do |tv|
+        puts l+"\t Effect: "+tv.consequence_type+" -- "+tv.transcript_stable_id.to_s
+      end                       
+    end
+  end 
+end
+
+
+def show_help()
+  puts "\nRuby Ensembl API -- Variation Effects Predictor"
+  puts "\n\tUSAGE: variation_effect_predictor -i variations.txt [OPTIONS]\n\n"
+  puts "\tOPTIONS:\n"
+  puts "\t\t-i\t Input file (Tab separated) REQUIRED"
+  puts "\t\t-s\t Species in snake case (default is 'homo_sapiens')"
+  puts "\t\t-r\t Ensembl Database release (default is 60)"
+  puts "\t\t-d\t Ensembl Database Server (default is 'ensembldb.ensembl.org')"
+  puts "\t\t-u\t Ensembl Database username (default is 'anonymous')"
+  puts "\t\t-p\t Ensembl Database password (only required for local Ensembl database)"
+  puts "\t\t-P\t Ensembl Database MySQL port connection (only required for local Ensembl database)"
+  puts "\t\t-g\t Connects to Ensembl Genomes Server (default is 'mysql.ebi.ac.uk')"
+  puts "\t\t-h\t Show this help"
+  puts "\n\n"
+end
+
+
+def get_consequence(chr,start,stop,alleles,strand,name)
+  variation = VariationFeature.new(:seq_region_id => SeqRegion.find_by_name(chr).seq_region_id,
+                                   :seq_region_start => start, 
+                                   :seq_region_end => stop, 
+                                   :allele_string => alleles, 
+                                   :seq_region_strand => strand, 
+                                   :variation_name => name
+                                   )
+  return variation.transcript_variations
+end
+
+
+
+run_calculations(ARGV)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

data/bio-ensembl.gemspec

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+# 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 = "bio-ensembl"
+  s.version = "1.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Jan Aerts", "Francesco Strozzi"]
+  s.date = "2011-12-06"
+  s.description = "This API provides a complete set of methods and classes to access the Ensembl database using Ruby programming language"
+  s.email = ["jan.aerts@gmail.com", "francesco.strozzi@gmail.com"]
+  s.executables = ["ensembl", "variation_effect_predictor"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/ensembl",
+    "bin/variation_effect_predictor",
+    "bio-ensembl.gemspec",
+    "lib/bio-ensembl.rb",
+    "lib/bio-ensembl/core/activerecord.rb",
+    "lib/bio-ensembl/core/collection.rb",
+    "lib/bio-ensembl/core/project.rb",
+    "lib/bio-ensembl/core/slice.rb",
+    "lib/bio-ensembl/core/transcript.rb",
+    "lib/bio-ensembl/core/transform.rb",
+    "lib/bio-ensembl/db_connection.rb",
+    "lib/bio-ensembl/variation/activerecord.rb",
+    "lib/bio-ensembl/variation/variation_feature.rb",
+    "lib/bio-ensembl/variation/variation_feature62.rb",
+    "samples/ensembl_genomes_example.rb",
+    "samples/examples_perl_tutorial.rb",
+    "samples/small_example_ruby_api.rb",
+    "samples/variation_effect_predictor_data.txt",
+    "samples/variation_example.rb",
+    "test/data/seq_c6qbl.fa",
+    "test/data/seq_cso19_coding.fa",
+    "test/data/seq_cso19_transcript.fa",
+    "test/data/seq_drd3_gene.fa",
+    "test/data/seq_drd3_transcript.fa",
+    "test/data/seq_drd4_transcript.fa",
+    "test/data/seq_forward_composite.fa",
+    "test/data/seq_par_boundary.fa",
+    "test/data/seq_rnd3_transcript.fa",
+    "test/data/seq_ub2r1_coding.fa",
+    "test/data/seq_ub2r1_gene.fa",
+    "test/data/seq_ub2r1_transcript.fa",
+    "test/data/seq_y.fa",
+    "test/default/test_connection.rb",
+    "test/default/test_releases.rb",
+    "test/ensembl_genomes/test_collection.rb",
+    "test/ensembl_genomes/test_gene.rb",
+    "test/ensembl_genomes/test_slice.rb",
+    "test/ensembl_genomes/test_variation.rb",
+    "test/helper.rb",
+    "test/release_50/core/test_project.rb",
+    "test/release_50/core/test_project_human.rb",
+    "test/release_50/core/test_relationships.rb",
+    "test/release_50/core/test_sequence.rb",
+    "test/release_50/core/test_slice.rb",
+    "test/release_50/core/test_transcript.rb",
+    "test/release_50/core/test_transform.rb",
+    "test/release_50/variation/test_activerecord.rb",
+    "test/release_50/variation/test_variation.rb",
+    "test/release_53/core/test_gene.rb",
+    "test/release_53/core/test_project.rb",
+    "test/release_53/core/test_project_human.rb",
+    "test/release_53/core/test_slice.rb",
+    "test/release_53/core/test_transform.rb",
+    "test/release_53/variation/test_activerecord.rb",
+    "test/release_53/variation/test_variation.rb",
+    "test/release_56/core/test_gene.rb",
+    "test/release_56/core/test_project.rb",
+    "test/release_56/core/test_slice.rb",
+    "test/release_56/core/test_transform.rb",
+    "test/release_56/variation/test_activerecord.rb",
+    "test/release_56/variation/test_consequence.rb",
+    "test/release_56/variation/test_variation.rb",
+    "test/release_60/core/test_gene.rb",
+    "test/release_60/core/test_project_human.rb",
+    "test/release_60/core/test_slice.rb",
+    "test/release_60/core/test_transcript.rb",
+    "test/release_60/core/test_transform.rb",
+    "test/release_60/variation/test_activerecord.rb",
+    "test/release_60/variation/test_consequence.rb",
+    "test/release_60/variation/test_variation.rb",
+    "test/release_62/core/test_gene.rb",
+    "test/release_62/variation/test_activerecord.rb",
+    "test/release_62/variation/test_consequence.rb"
+  ]
+  s.homepage = "http://github.com/fstrozzi/bioruby-ensembl"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.12"
+  s.summary = "A Ruby API to the Ensembl database"
+  s.test_files = [
+    "test/default/test_connection.rb",
+    "test/default/test_releases.rb",
+    "test/ensembl_genomes/test_collection.rb",
+    "test/ensembl_genomes/test_gene.rb",
+    "test/ensembl_genomes/test_slice.rb",
+    "test/ensembl_genomes/test_variation.rb",
+    "test/helper.rb",
+    "test/release_50/core/test_project.rb",
+    "test/release_50/core/test_project_human.rb",
+    "test/release_50/core/test_relationships.rb",
+    "test/release_50/core/test_sequence.rb",
+    "test/release_50/core/test_slice.rb",
+    "test/release_50/core/test_transcript.rb",
+    "test/release_50/core/test_transform.rb",
+    "test/release_50/variation/test_activerecord.rb",
+    "test/release_50/variation/test_variation.rb",
+    "test/release_53/core/test_gene.rb",
+    "test/release_53/core/test_project.rb",
+    "test/release_53/core/test_project_human.rb",
+    "test/release_53/core/test_slice.rb",
+    "test/release_53/core/test_transform.rb",
+    "test/release_53/variation/test_activerecord.rb",
+    "test/release_53/variation/test_variation.rb",
+    "test/release_56/core/test_gene.rb",
+    "test/release_56/core/test_project.rb",
+    "test/release_56/core/test_slice.rb",
+    "test/release_56/core/test_transform.rb",
+    "test/release_56/variation/test_activerecord.rb",
+    "test/release_56/variation/test_consequence.rb",
+    "test/release_56/variation/test_variation.rb",
+    "test/release_60/core/test_gene.rb",
+    "test/release_60/core/test_project_human.rb",
+    "test/release_60/core/test_slice.rb",
+    "test/release_60/core/test_transcript.rb",
+    "test/release_60/core/test_transform.rb",
+    "test/release_60/variation/test_activerecord.rb",
+    "test/release_60/variation/test_consequence.rb",
+    "test/release_60/variation/test_variation.rb",
+    "test/release_62/core/test_gene.rb",
+    "test/release_62/variation/test_activerecord.rb",
+    "test/release_62/variation/test_consequence.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_runtime_dependency(%q<mysql>, [">= 0"])
+      s.add_runtime_dependency(%q<activerecord>, ["= 3.0.0"])
+      s.add_development_dependency(%q<shoulda>, [">= 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_development_dependency(%q<mysql>, [">= 0"])
+      s.add_development_dependency(%q<activerecord>, ["= 3.0.0"])
+    else
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<mysql>, [">= 0"])
+      s.add_dependency(%q<activerecord>, ["= 3.0.0"])
+      s.add_dependency(%q<shoulda>, [">= 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<mysql>, [">= 0"])
+      s.add_dependency(%q<activerecord>, ["= 3.0.0"])
+    end
+  else
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<mysql>, [">= 0"])
+    s.add_dependency(%q<activerecord>, ["= 3.0.0"])
+    s.add_dependency(%q<shoulda>, [">= 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<mysql>, [">= 0"])
+    s.add_dependency(%q<activerecord>, ["= 3.0.0"])
+  end
+end
+