Class: Ensembl::Core::Gene

Inherits:
DBConnection show all
Includes:
Sliceable
Defined in:
lib/bio-ensembl/core/activerecord.rb

Overview

The Gene class provides an interface to the gene table. This table contains mappings of genes to a SeqRegion.

This class uses ActiveRecord to access data in the Ensembl database. See the general documentation of the Ensembl module for more information on what this means and what methods are available.

This class includes the mixin Sliceable, which means that it is mapped to a SeqRegion object and a Slice can be created for objects of this class. See Sliceable and Slice for more information.

Examples:

puts Gene.find_by_biotype('protein_coding').length

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Sliceable

#length, #project, #seq, #slice, #start, #stop, #strand, #transform

Methods inherited from DBConnection

connect, ensemblgenomes_connect

Methods inherited from DBRegistry::Base

generic_connect, get_info, get_name_from_db

Class Method Details

.find_all_by_name(name) ⇒ Object

The Gene#find_all_by_name class method searches the Xrefs for that name and returns an array of the corresponding Gene objects. If the name is not found, it returns an empty array.



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1067

def self.find_all_by_name(name)
	answer = Array.new
  xrefs = Ensembl::Core::Xref.find_all_by_display_label(name)
  xrefs.each do |xref|
    answer.push(Ensembl::Core::Gene.find_by_display_xref_id(xref.xref_id))
  end
  
  answer.reject!{|a| a.nil?}
	return answer
end

.find_by_name(name) ⇒ Object

The Gene#find_by_name class method searches the Xrefs for that name and returns one Gene objects (even if there should be more). If the name is not found, it returns nil.



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1081

def self.find_by_name(name)
  all_names = self.find_all_by_name(name)
  if all_names.length == 0
    return nil
  else
    return all_names[0]
  end
end

.find_by_stable_id(stable_id) ⇒ Object

The Gene#find_by_stable_id class method fetches a Gene object based on its stable ID (i.e. the “ENSG” accession number). If the name is not found, it returns nil.



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1093

def self.find_by_stable_id(stable_id)
  result = nil
  if stable_id.kind_of? Array
    gene_stable_ids = GeneStableId.where({:stable_id => stable_id})
    result = (gene_stable_ids.size == 0) ? nil : gene_stable_ids.map {|id| id.gene}
  else
    gene_stable_id = GeneStableId.find_by_stable_id(stable_id)
    result = (gene_stable_id.nil?) ? nil : gene_stable_id.gene
  end
  return result
end

Instance Method Details

#all_xrefs ⇒ Object

The Gene#all_xrefs method is a convenience method in that it combines three methods into one. It collects all xrefs for the gene itself, plus all xrefs for all transcripts for the gene, and all xrefs for all translations for those transcripts.



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1109

def all_xrefs
  answer = Array.new
  answer.push(self.xrefs)
  self.transcripts.each do |transcript|
    answer.push(transcript.xrefs)
    if ! transcript.translation.nil?
      answer.push(transcript.translation.xrefs)
    end
  end
  answer.flatten!
  return answer
end

#display_label ⇒ Object Also known as: display_name, label, name

The Gene#display_label method returns the default name of the gene.



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1057

def display_label
  return Xref.find(self.display_xref_id).display_label
end

#go_terms ⇒ Object

The Gene#go_terms method returns all GO terms associated with a gene.



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1123

def go_terms
  go_db_id = ExternalDb.find_by_db_name('GO').id
  return self.all_xrefs.select{|x| x.external_db_id == go_db_id}.collect{|x| x.dbprimary_acc}.uniq
end

#hgnc ⇒ Object

The Gene#hgnc returns the HGNC symbol for the gene.



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1129

def hgnc
  hgnc_db_id = ExternalDb.find_by_db_name('HGNC_curated_gene').id
  xref = self.all_xrefs.select{|x| x.external_db_id == hgnc_db_id}[0]
  return nil if xref.nil?
  return xref.display_label
end

#stable_id ⇒ Object

The Gene#stable_id method returns the stable_id of the gene (i.e. the ENSG id).



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# File 'lib/bio-ensembl/core/activerecord.rb', line 1051

def stable_id
  return self.gene_stable_id.stable_id
	
end