Module: Mutation::Oncotate

Included in:
Mutation
Defined in:
lib/oncotator.rb

Instance Method Summary collapse

Instance Method Details

#discard_onco ⇒ Object 



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# File 'lib/oncotator.rb', line 157

def discard_onco
  @onco = nil
end

#in_cosmic ⇒ Object 



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# File 'lib/oncotator.rb', line 165

def in_cosmic
  onco.Cosmic_overlapping_mutations ? "YES" : "NO"
end

#inspect ⇒ Object 



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# File 'lib/oncotator.rb', line 161

def inspect
  "#<#{self.class.name}:#{object_id} @mutation=#{@mutation}>"
end

#onco ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/oncotator.rb', line 152

def onco
  raise ArgumentError, @onco_error unless valid_onco_input?
  @onco ||= Oncotator.new :key => to_ot
end

#to_ot ⇒ Object 



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# File 'lib/oncotator.rb', line 169

def to_ot
  [ short_chrom, start, stop, ref, alt ].join("_")
end