Class: Ensembl::Variation::Variation

Inherits:
ModelBase show all
Defined in:
lib/ensembl/variation/activerecord.rb

Class Method Summary collapse

Instance Method Summary collapse

Methods included from PrimaryKeyOverrides

#primary_key

Methods included from TableNameOverrides

#table_name

Class Method Details

.find_all_by_name(name) ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 604

def self.find_all_by_name(name)
  v_ids = where(name: name).pluck(:variation_id)
  v_ids = variation_synonyms.where(name: name).pluck(:variation_id) if v_ids.nil?

  return nil if v_ids.nil?

  where(variation_id: v_ids).order(:name)
end

.find_by_name(name) ⇒ Object

Find Variation by also using VariationSynonyms @name: name of the variation @return: [Variation]



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# File 'lib/ensembl/variation/activerecord.rb', line 596

def self.find_by_name(name)
  v  = self.find_by(name: name)
  return v unless v.nil?
  vs = VariationSynonym.eager_load(:variation).find_by(name: name)
  return vs.variation unless vs.nil?
  nil
end

Instance Method Details

#all_phenotype_features ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 506

def all_phenotype_features
  object_ids = synonym_names
  object_ids<<name
  PhenotypeFeature.eager_load(:phenotype).where(object_id: object_ids, type: 'Variation')
end

#genes ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 613

def genes
  variation_genenames.pluck(:gene_name)
end

#genotype_code_ids ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 583

def genotype_code_ids
  @genotype_code_ids||=individual_genotypes.values.uniq
end

#genotype_codes ⇒ Object

Unique genotype codes from individual_genotypes



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# File 'lib/ensembl/variation/activerecord.rb', line 589

def genotype_codes
  @genotype_codes||=GenotypeCode.genotypes_hash_for(genotype_code_ids)
end

#genotype_counts ⇒ Object

Genotype counts for each population “CSHL-HAPMAP:HapMap-YRI”=>“C|T”=>1}



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# File 'lib/ensembl/variation/activerecord.rb', line 557

def genotype_counts
  counts = Hash.new{ |hsh,k| hsh[k] = Hash.new 0 }

  individual_populations.pluck('population.name',:individual_id).map{|ip| [ip[0],genotype_codes[individual_genotypes[ip[1]]]] }.each{|r| counts[r[0]][r[1]]+=1}

  return counts
end

#individual_genotype_ids ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 573

def individual_genotype_ids
  individual_genotypes.keys
end

#individual_genotypes ⇒ Object

Individual and genotype_code id’s related to variation Example:

[1,2],,[<individual_id>,<genotype_code_id>] 


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# File 'lib/ensembl/variation/activerecord.rb', line 569

def individual_genotypes
  @individual_genotypes||=compressed_genotype_vars.map{|cgv| cgv.unpacked_genotypes }.flatten(1).to_h
end

#individual_populations ⇒ Object

IndividualPopulations from individual_genotypes



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# File 'lib/ensembl/variation/activerecord.rb', line 579

def individual_populations
  IndividualPopulation.where(individual_id: individual_genotype_ids)
end

#phenotype_features ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 502

def phenotype_features
  PhenotypeFeature.eager_load(:phenotype).where(object_id_column: name, type: 'Variation')
end

#phenotype_features_hash ⇒ Object

Made because of the need to cut down database queries { phenotype_feature_id =>

 { :phenotype=> "Phenotype description" ,
   :phenotype_id => _ ,
   :p_value => _ ,
   :odds_ratio => _,
   :risk_allele => _ },
phenotype_feature_id =>
 { :phenotype=> "Phenotype description" ,
   :phenotype_id => _ ,
   :p_value => _ ,
   :odds_ratio => _,
   :risk_allele => _ }}

Returns:



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# File 'lib/ensembl/variation/activerecord.rb', line 526

def phenotype_features_hash

  # Do enable two level inserts hsh[:first][:second]
  hash=Hash.new{ |hsh,key| hsh[key] = Hash.new {} }

  all_phenotype_features
  .joins(:phenotype)
  .pluck(
      :phenotype_feature_id,
      'phenotype.description',
      :phenotype_id)
  .each{ |r| hash[r[0]][:phenotype]=r[1]; hash[r[0]][:phenotype_id]=r[2]}

  PhenotypeFeatureAttrib
  .where(phenotype_feature_id: hash.keys)
  .pluck(
      'phenotype_feature_attrib.phenotype_feature_id',
      'phenotype_feature_attrib.value',
      'phenotype_feature_attrib.attrib_type_id')
  .each{ |v| hash[v[0]][AttribType.symbol(v[2])]=v[1] }

  hash
end

#positions ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 617

def positions
  variation_features.includes(:seq_region).pluck('seq_region.name',:seq_region_start,:seq_region_end,:seq_region_strand).map{|r| Ensembl::Helpers::VariationPosition.new(r)}
end

#synonym_names ⇒ Object 



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# File 'lib/ensembl/variation/activerecord.rb', line 550

def synonym_names
  variation_synonyms.map{|vs| vs.name}
end