ensembl 0.0.4 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/ensembl.gemspec

@@ -22,6 +22,7 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency 'mysql2', '~> 0.3'
   spec.add_dependency 'activerecord', '~> 4.1'
+  spec.add_dependency 'activerecord-tableless', '~> 1.0'
 
   spec.add_development_dependency "bundler", "~> 1.6"
   spec.add_development_dependency "rake", '~> 10.3'

data/lib/ensembl/core/activerecord.rb

@@ -1,5 +1,6 @@
 module Ensembl
   module Core
+
     module StableIdHistory
       def previous_stable_ids
         StableIdEvent.where(new_stable_id: stable_id)

data/lib/ensembl/variation/activerecord.rb

@@ -47,7 +47,6 @@ module Ensembl
 
     class AttribSet < ModelBase
       belongs_to :attrib
-
     end
 
     class AttribType < ModelBase
@@ -66,6 +65,32 @@ module Ensembl
       belongs_to :variation
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
 
+      def individual_genotypes
+        nil if genotypes.nil?
+
+        # To decrease number of DB queries needed
+        # FIXME: Should be in GenotypeCodes class or should use caching
+        genotype_codes=genotype_code_ids.uniq.inject({}) { |hsh, gc_id | hsh[gc_id]=GenotypeCode.find gc_id;hsh  }
+
+        @igs||=unpacked_genotypes.map{|s| IndividualGenotype.new({ individual_id:  s[0],genotype_code_id:s[1]})}
+      end
+
+      def unpacked_genotypes
+        unpack_genotypes.each_slice(2).map{|sl| sl }
+      end
+
+      def individual_ids
+        unpack_genotypes.select.each_with_index{|str,i| i.even?}
+      end
+
+      def genotype_code_ids
+        unpack_genotypes.select.each_with_index{|str,i| i.odd?}
+      end
+
+      protected
+      def unpack_genotypes
+        @g_unpacked||=genotypes.unpack('ww*') unless genotypes.nil?
+      end
     end
 
     class CoordSystem < ModelBase
@@ -95,8 +120,8 @@ module Ensembl
     end
 
     class GenotypeCode < ModelBase
+
       belongs_to :allele_code
-      belongs_to :genotype_code
 
     end
 
@@ -177,29 +202,26 @@ module Ensembl
     class PhenotypeFeatureAttrib < Connection
       belongs_to :attrib_type
       belongs_to :phenotype_feature
-
     end
 
     class Population < ModelBase
       self.extend Ensembl::SearchByName
 
-      has_many :population_synonyms
-      #has_many :synonyms, through: :population_synonyms, source: :synonym
       has_many :alleles
+      has_many :population_synonyms
 
       has_many :individual_populations
       has_many :individuals, through: :individual_populations
 
-      has_many :population_structures, foreign_key: 'super_population_id'
+      has_many :sub_population_structures, foreign_key: 'super_population_id', class_name: 'PopulationStructure'
       has_many :sub_populations, through: :population_structures, source: :sub_population
-      has_many :parents, through: :population_structures, source: :super_populaton#, foreign_key: 'sub_population_id'
+
+      has_many :super_population_structures, foreign_key: 'sub_population_id', class_name: 'PopulationStructure'
+      has_many :super_populations, through: :population_structures, source: :super_populaton
 
       has_many :population_genotypes
 
-      def parent
-        ps=PopulationStructure.find_by(sub_population: id)
-        ps.super_population unless ps.nil?
-      end
+      scope :displayable, -> { where(display:'LD')}
 
       def all_individual_populations
         IndividualPopulation.where(population_id: sub_population_ids(self)<<id)
@@ -233,8 +255,8 @@ module Ensembl
       belongs_to :variation
       belongs_to :population
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
-
       belongs_to :genotype_code
+
       has_one :allele_code, through: :genotype_code
     end
 
@@ -309,10 +331,10 @@ module Ensembl
     class StructuralVariationSample < ModelBase
       belongs_to :structural_variation
       belongs_to :individual
+      belongs_to :strain, foreign_key: 'strain_id', class_name: 'Individual'
     end
 
     class Source < ModelBase
-
     end
 
     class Study < ModelBase
@@ -449,7 +471,6 @@ module Ensembl
       belongs_to :short_name, foreign_key: 'short_name_attrib_id', class_name: 'Attrib'
       has_many :structural_variations
 
-      #has_many :variation_set_structures, foreign_key: 'variation_set_super'
       has_many :sub_variation_set_structures, foreign_key: 'variation_set_super', class_name: 'VariationSetStructure'
       has_many :sub_variation_sets, through: :sub_variation_set_structures , source: :sub_variation_set
 

data/lib/ensembl/variation/tableless.rb

@@ -0,0 +1,22 @@
+require 'active_record'
+require 'activerecord-tableless'
+
+module Ensembl
+  module Variation
+    class IndividualGenotype < ActiveRecord::Base
+      has_no_table
+
+      column :individual_id, :integer
+      column :genotype_code_id, :integer
+
+      belongs_to :individual
+      belongs_to :genotype_code
+
+      has_one :allele_code, through: :genotype_code
+
+      delegate :individual_populations, to: :individual
+      delegate :populations, to: :individual
+
+    end
+  end
+end

data/lib/ensembl/version.rb

@@ -1,3 +1,3 @@
 module Ensembl
-  VERSION = "0.0.4"
+  VERSION = '0.0.5'
 end

data/lib/ensembl.rb

@@ -110,3 +110,4 @@ end
 
 require File.dirname(__FILE__) + '/ensembl/core/activerecord.rb'
 require File.dirname(__FILE__) + '/ensembl/variation/activerecord.rb'
+require File.dirname(__FILE__) + '/ensembl/variation/tableless.rb'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ensembl
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - Kristjan Metsalu
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-22 00:00:00.000000000 Z
+date: 2014-07-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: mysql2
@@ -38,6 +38,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '4.1'
+- !ruby/object:Gem::Dependency
+  name: activerecord-tableless
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -96,6 +110,7 @@ files:
 - lib/ensembl.rb
 - lib/ensembl/core/activerecord.rb
 - lib/ensembl/variation/activerecord.rb
+- lib/ensembl/variation/tableless.rb
 - lib/ensembl/version.rb
 homepage: https://github.com/kmetsalu/ensembl
 licenses: