ensembl 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
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+  data.tar.gz: d5251a5716e27400796a2b9965e0549faa184576
+SHA512:
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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log
+
+.idea

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in ensembl.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2014 Kristjan Metsalu
+
+MIT License
+
+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.md

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+# Ensembl
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'ensembl'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install ensembl
+
+## Usage
+
+    require 'ensembl'
+
+### ENSEMBL.ORG database - Default configuration
+    
+    Ensembl::Variation::Variation.first
+    
+    Ensembl::Variation::Variation.first.source
+
+### Custom database
+    
+    # Set following values before using
+    
+    Ensembl.host = 'myhost.example.com'
+    Ensembl.port = 3306                                 # default
+    Ensembl.username = 'anonymous'                      # default
+    Ensembl.password = ''                               # default
+    Ensembl.database = 'homo_sapiens_variation_75_37'   # default
+
+
+## Contributing
+
+1. Fork it ( https://github.com/kmetsalu/ensembl/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+
+task :console do
+  exec "irb -r ensembl -I ./lib"
+end
+

data/ensembl.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ensembl/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "ensembl"
+  spec.version       = Ensembl::VERSION
+  spec.authors       = ["Kristjan Metsalu"]
+  spec.email         = ["kristjan.metsalu@ut.ee"]
+  spec.summary       = %q{ Gem to access Ensembl.org databases through API }
+  spec.description   = %q{ If it gets better than summary then I'm gonna add it }
+  spec.homepage      = "https://github.com/kmetsalu/ensembl"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency 'mysql2', '~> 0.3'
+  spec.add_dependency 'activerecord', '~> 4.1'
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake", '~> 10.3'
+end

data/lib/ensembl/variation/activerecord.rb

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+require 'active_record'
+
+module Ensembl
+  module Variation
+    class Allele < Ensembl::ModelBase
+      belongs_to :variation
+      belongs_to :population
+      belongs_to :subsnp_handle
+      belongs_to :allele_code
+
+    end
+
+    class AlleleCode < Ensembl::ModelBase
+      has_many :genotype_codes
+
+    end
+
+    class AssociateStudy < Ensembl::Connection
+      belongs_to :study, foreign_key: 'study1_id', class_name: 'Study'
+      belongs_to :associated_study, foreign_key: 'study2_id', class_name: 'Study'
+
+    end
+
+    class Attrib < Ensembl::ModelBase
+      belongs_to :attrib_type
+
+    end
+
+    class AttribSet < Ensembl::ModelBase
+      belongs_to :attrib
+
+    end
+
+    class AttribType < Ensembl::ModelBase
+      has_many :attribs, class_name: 'Attrib'
+      has_many :pheotype_feature_attrib
+      has_many :phenotype_features, through: :phenotype_feature_attrib
+
+    end
+
+    class CompressedGenotypeRegion < Ensembl::Connection
+      belongs_to :individual
+
+    end
+
+    class CompressedGenotypeVar < Ensembl::Connection
+      belongs_to :variation
+      belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
+
+    end
+
+    class CoordSystem < Ensembl::ModelBase
+    end
+
+    class FailedAllele < Ensembl::ModelBase
+      belongs_to :failed_description
+      belongs_to :allele
+
+    end
+
+    class FailedDescription < Ensembl::ModelBase
+      belongs_to :failed_variation
+
+    end
+
+    class FailedStructuralVariation < Ensembl::ModelBase
+      belongs_to :structural_variation
+      belongs_to :failed_description
+
+    end
+
+    class FailedVariation < Ensembl::ModelBase
+      belongs_to :variation
+      has_one :failed_description
+
+    end
+
+    class GenotypeCode < Ensembl::ModelBase
+      belongs_to :allele_code
+      belongs_to :genotype_code
+
+    end
+
+    class Individual < Ensembl::ModelBase
+      belongs_to :individual_type
+      belongs_to :father, foreign_key: 'father_individual_id', class_name: 'Individual'
+      belongs_to :mother, foreign_key: 'mother_individual_id', class_name: 'Individual'
+
+      has_many :individual_populations
+      has_many :populations, through: :individual_populations
+
+      has_many :individual_synonyms, foreign_key: :synonym_id
+      has_many :synonyms, through: :individual_synonyms
+
+      scope :with_fathers, -> { where.not(father:nil) }
+      scope :with_mothers, -> { where.not(mother:nil) }
+
+    end
+
+    class IndividualGenotypeMultipleBp < Ensembl::Connection
+      belongs_to :variation
+      belongs_to :individual
+      belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
+
+    end
+
+    class IndividualPopulation < Ensembl::Connection
+      belongs_to :individual
+      belongs_to :population
+
+    end
+
+    class IndividualSynonym < Ensembl::Connection
+      belongs_to :individual
+      belongs_to :source
+      belongs_to :synonym, class_name: 'Individual'
+
+    end
+
+    class IndividualType < Ensembl::ModelBase
+      has_many :individuals
+    end
+
+    class Meta < Ensembl::ModelBase
+      # TODO: Link with others
+    end
+
+    class MetaCoord < Ensembl::Connection
+    end
+
+    class MotifFreatureVariation < Ensembl::ModelBase
+      belongs_to :variation_feature
+    end
+
+    class Phenotype < Ensembl::ModelBase
+      has_many :phenotype_features
+    end
+
+    class PhenotypeFeature < Ensembl::ModelBase
+      # Hack because using type column in the database
+      self.inheritance_column = ':_no_inheritance_column'
+
+      belongs_to :phenotype
+      belongs_to :source
+      belongs_to :study
+
+      has_many :phenotype_feature_attrib
+      has_many :attrib_types, through: :phenotype_feature_attrib
+
+      def variation
+        Variation.find_by name: object_id
+      end
+
+    end
+
+    class PhenotypeFeatureAttrib < Ensembl::Connection
+      belongs_to :attrib_type
+      belongs_to :phenotype_feature
+
+    end
+
+    class Population < Ensembl::ModelBase
+      has_many :population_synonyms
+      has_many :synonyms, through: :population_synonyms, source: :synonym
+      has_many :alleles
+
+      has_many :individual_populations
+      has_many :individuals, through: :individual_populations
+
+      has_many :population_structures, foreign_key: 'super_population_id'
+      has_many :sub_populations, through: :population_structures, source: :sub_population
+
+      has_many :population_genotypes
+
+      def all_individual_populations
+        IndividualPopulation.where(population_id: sub_populations.pluck(:population_id))
+      end
+
+      def all_individuals
+        Individual.where individual_id: all_individual_populations.pluck(:individual_id)
+      end
+
+    end
+
+    class PopulationSynonym < Ensembl::Connection
+      belongs_to :synonym, foreign_key: 'synonym_id', class_name: 'Population'
+      belongs_to :population
+      belongs_to :source
+    end
+
+    class PopulationGenotype < Ensembl::ModelBase
+      belongs_to :variation
+      belongs_to :population
+      belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
+      belongs_to :genotype_code
+
+    end
+
+    class PopulationStructure < Ensembl::Connection
+      belongs_to :population, foreign_key: 'super_population_id', class_name: 'Population'
+      belongs_to :sub_population, foreign_key: 'sub_population_id', class_name: 'Population'
+
+    end
+
+    class ProteinFunctionPredictions < Ensembl::Connection
+    end
+
+    class Publication < Ensembl::ModelBase
+    end
+
+    class RegulatoryFeatureVariation < Ensembl::ModelBase
+      belongs_to :variation_feature
+
+    end
+
+    class SeqRegion < Ensembl::ModelBase
+      belongs_to :coord_system
+
+    end
+
+    class StrainGtypePoly < Ensembl::Connection
+      belongs_to :variation
+
+    end
+
+    class StructuralVariation < Ensembl::ModelBase
+      belongs_to :source
+      belongs_to :study
+
+      belongs_to :class_attrib, foreign_key: 'class_attrib_id', class_name: 'Attrib'
+      has_one :classification, through: :class_attrib, source: :attrib_type
+
+      belongs_to :clinical_significance_attrib, foreign_key: 'clinical_significance_id', class_name: 'Attrib'
+      has_one :clinical_significance, through: :clinical_significance_attrib, source: :attrib_type
+
+      has_many :structural_variation_associations
+      has_many :supporting_structural_variations, through: :structural_variation_associations
+
+      has_many :structural_variation_samples
+      has_many :individuals, through: :structural_variation_samples, source: :individual
+
+      has_many :variation_sets
+
+      scope :with_supporting_structural_variations, -> { joins(:structural_variation_associations).where.not structural_variation_associations: nil }
+
+    end
+
+    class StructuralVariationAssociation < Ensembl::Connection
+      belongs_to :structural_variation
+      belongs_to :supporting_structural_variation, foreign_key: 'supporting_structural_variation_id', class_name: 'StructuralVariation'
+    end
+
+    class StructuralVariationFeature < Ensembl::ModelBase
+      belongs_to :seq_region
+      belongs_to :structural_variation
+      belongs_to :source
+      belongs_to :study
+      belongs_to :variation_set
+
+      belongs_to :class_attrib, foreign_key: 'class_attrib_id', class_name: 'Attrib'
+      has_one :classification, through: :class_attrib, source: :attrib_type
+
+    end
+
+    class StructuralVariationSample < Ensembl::ModelBase
+      belongs_to :structural_variation
+      belongs_to :individual
+    end
+
+    class Study < Ensembl::ModelBase
+      has_many :study_variations
+      has_many :variations, through: :study_variations
+
+    end
+
+    class Source < Ensembl::ModelBase
+
+    end
+
+    class Study < Ensembl::ModelBase
+      has_many :associate_studies, foreign_key: 'study1_id'
+      has_many :associated_studies, through: :associate_studies, source: :associated_study
+
+      # FIXME: No data in database
+      has_many :variations, through: :study_variations
+    end
+
+    # FIXME: No data in database
+    class StudyVariation < Ensembl::Connection
+      belongs_to :study
+      belongs_to :variation
+    end
+
+    class SubmitterHandle < Ensembl::Connection
+      self.primary_key = 'handle_id'
+    end
+
+    class SubsnpHandle < Ensembl::Connection
+      self.primary_key = 'subsnp_id'
+
+      has_many :subsnp_maps
+    end
+
+    class SubsnpMap < Ensembl::Connection
+      belongs_to :variation
+      belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
+    end
+
+    class TaggedVariationFeature < Ensembl::ModelBase
+      belongs_to :variation_feature
+      belongs_to :population
+    end
+
+    class TranscriptVariation < Ensembl::ModelBase
+      belongs_to :variation_feature
+
+    end
+
+    class TranslationMd5 < Ensembl::ModelBase
+
+    end
+
+    class Variation < Ensembl::ModelBase
+      belongs_to :source
+      has_many :variation_synonyms
+      has_many :failed_variations
+      has_many :alleles
+      has_many :population_genotypes
+      has_many :study_variations
+      has_many :studies, through: :study_variations
+      has_many :variation_citations
+      has_many :publications, through: :variation_citations
+      has_many :subsnp_maps
+      has_many :variation_genenames
+      has_many :variation_hgvs, class_name: 'VariationHgvs'
+      has_many :variation_sets
+
+      def phenotype_features
+        PhenotypeFeature.where(object_id: name, type: 'Variation')
+      end
+
+      def all_phenotype_features
+        object_ids = variation_synonyms.pluck :name
+        object_ids<<name
+        PhenotypeFeature.where(object_id: object_ids, type: 'Variation')
+      end
+    end
+
+    class VariationCitation < Ensembl::Connection
+      self.table_name = 'variation_citation'
+      belongs_to :variation
+      belongs_to :publication
+    end
+
+    class VariationFeature < Ensembl::ModelBase
+      belongs_to :variation
+      belongs_to :source
+      has_many :transcript_variations
+      has_many :motif_freature_variations
+      has_many :tagged_variation_features
+
+    end
+
+    class VariationGenename < Ensembl::Connection
+      belongs_to :variation
+    end
+
+    class VariationHgvs < Ensembl::Connection
+      belongs_to :variation
+    end
+
+    class VariationSet < Ensembl::ModelBase
+      belongs_to :short_name, foreign_key: 'short_name_attrib_id', class_name: 'Attrib'
+      has_many :structural_variations
+
+      has_many :variation_set_structures
+      has_many :sub_variation_sets, through: :variation_set_structures, source: :sub_variation_set
+
+      has_many :variations
+    end
+
+    class VariationSetStructuralVariation < Ensembl::Connection
+      belongs_to :structural_variation
+      belongs_to :variation_set
+    end
+
+    class VariationSetStructure < Ensembl::Connection
+      belongs_to :super_variation_set, foreign_key: 'super_variation_set_id', class_name: 'VariationSet'
+      belongs_to :sub_variation_set, foreign_key: 'sub_variation_set_id', class_name: 'VariationSet'
+    end
+
+    class VariationSetVariation < Ensembl::Connection
+      belongs_to :variation
+      belongs_to :variation_set
+    end
+
+    class VariationSynonym < Ensembl::ModelBase
+      belongs_to :variation
+      belongs_to :source
+    end
+
+
+  end
+end

data/lib/ensembl/version.rb

@@ -0,0 +1,3 @@
+module Ensembl
+  VERSION = "0.0.1"
+end

data/lib/ensembl.rb

@@ -0,0 +1,65 @@
+require "ensembl/version"
+require 'active_record'
+require 'active_support/core_ext'
+
+module Ensembl
+
+  class << self
+
+    attr_accessor :host, :port, :database, :username, :password
+
+    def host
+      @host||='ensembldb.ensembl.org'
+    end
+
+    def port
+      @port||=3306
+    end
+
+    def username
+      @username||='anonymous'
+    end
+
+    def password
+      @password||=''
+    end
+
+    def database
+      @database||='homo_sapiens_variation_75_37'
+    end
+
+  end
+
+  module TableNameOverrides
+    def table_name
+      self.name.split('::').last.underscore || ''
+    end
+  end
+
+  module PrimaryKeyOverrides
+    def primary_key
+      self.table_name + '_id'
+    end
+  end
+
+  class Connection < ActiveRecord::Base
+    self.extend TableNameOverrides
+
+    self.abstract_class = true
+
+    self.establish_connection :adapter  => "mysql2",
+                              :host     => Ensembl.host,
+                              :username => Ensembl.username,
+                              :password => Ensembl.password,
+                              :database => Ensembl.database
+
+  end
+
+  class ModelBase < Connection
+    self.extend PrimaryKeyOverrides
+
+    self.abstract_class = true
+  end
+end
+
+require File.dirname(__FILE__) + '/ensembl/variation/activerecord.rb'

metadata

@@ -0,0 +1,109 @@
+--- !ruby/object:Gem::Specification
+name: ensembl
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Kristjan Metsalu
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-06-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: mysql2
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.3'
+- !ruby/object:Gem::Dependency
+  name: activerecord
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.1'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.3'
+description: " If it gets better than summary then I'm gonna add it "
+email:
+- kristjan.metsalu@ut.ee
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- ensembl.gemspec
+- lib/ensembl.rb
+- lib/ensembl/variation/activerecord.rb
+- lib/ensembl/version.rb
+homepage: https://github.com/kmetsalu/ensembl
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+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: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Gem to access Ensembl.org databases through API
+test_files: []