Class: Exodb::Cell

Inherits:
Source show all
Defined in:
lib/exodb/datamodel/source.rb

Direct Known Subclasses

Normal, Tumor

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.translate! ⇒ Object 


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# File 'lib/exodb/datamodel/source.rb', line 56

def self.translate!
	self.where({}).each {|e| e.translate!}
end

Instance Method Details

#add_to_dataset(str) ⇒ Object

get the start position of gene rely on the genome

Parameters:


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# File 'lib/exodb/datamodel/source.rb', line 63

def add_to_dataset(str)
	
	dataset = Dataset.where('$or' => [{'oid' => str}, {'name' => str}])
	
	if dataset.exists?
		self.dataset = dataset.first()
		#output.puts "#EXODUS:INFO This sample is added to #{dataset.first().name}." if $0 == 'pry'
	else
		#output.puts "#EXODUS:ERRO Cannot find dataset by #{str}."  if $0 == 'pry'
	end
end

#translate!(cutoff = 0) ⇒ Object

Translate variant

Parameters:

  • cutoff (Float) (defaults to: 0) —

    score


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# File 'lib/exodb/datamodel/source.rb', line 78

def translate!(cutoff = 0)
	self.variants.each do |variant|
		
		Generef.cover?(variant.location_str).each do |generef|
			
			if generef.can_translated?
				
				mainsplice = generef.longest_splice
				position = mainsplice.get_prot_pos(variant.start)
				
				if !position.empty?
					gene = self.genes.find_or_create_by({symbol: generef.symbol})
					gene.generef = generef
					aacid = gene.aacids.find_or_create_by({position: /\A[A-Z]#{position[0]}[A-Z]?\z/ =~ variant.aachange ? position[0] : variant.aachange.split(/(\d+)/)[1].to_i})
					aacid.refcodon = mainsplice.get_codon(position[0]) if !aacid.refcodon
					aacid.refaa = mainsplice.get_codon(position[0]).translate if !aacid.refaa
					aacid.altcodon = {} if !aacid.altcodon
					aacid.altcodon[position[1]]  = aacid.altcodon[position[1]] ? aacid.altcodon[position[:posincodon]] | variant.alternate : variant.alternate
					aacid.isoform = [] if !aacid.isoform
					aacid.variants.push(variant)
					
					generef.splices.each do |splice|
						position = splice.get_prot_pos(variant.start)
						aacid.isoform.push("#{generef.get_xref()}:p.#{mainsplice.get_codon(position[0]).translate}#{position[0]}") if !position.empty?
					end
					gene.save!
				end
			end
		end
	end
end