Class: Bio::SQL::Location

Inherits:
DummyBase show all
Defined in:
lib/bio/io/biosql/location.rb

Instance Method Summary collapse

Instance Method Details

#sequence ⇒ Object 



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# File 'lib/bio/io/biosql/location.rb', line 19

def sequence
  seq=""
  unless self.seqfeature.bioentry.biosequence.seq.nil?
    seq=Bio::Sequence::NA.new(self.seqfeature.bioentry.biosequence.seq[start_pos-1..end_pos-1])
    seq.reverse_complement! if strand==-1
  end
  return seq        
end

#to_s ⇒ Object 



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# File 'lib/bio/io/biosql/location.rb', line 10

def to_s
  if strand==-1
    str="complement("+start_pos.to_s+".."+end_pos.to_s+")"
  else
    str=start_pos.to_s+".."+end_pos.to_s
  end
  return str    
end