Class: Bio::FinishM::ConnectionInterpreter::Scaffold

Inherits:
Object
  • Object
show all
Defined in:
lib/assembly/connection_interpreter.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Scaffold

Returns a new instance of Scaffold.



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# File 'lib/assembly/connection_interpreter.rb', line 308

def initialize
  @contigs = []
  @gap_lengths = []
end

Instance Attribute Details

#circular ⇒ Object

Returns the value of attribute circular.



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# File 'lib/assembly/connection_interpreter.rb', line 303

def circular
  @circular
end

#contigs ⇒ Object

Returns the value of attribute contigs.



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# File 'lib/assembly/connection_interpreter.rb', line 301

def contigs
  @contigs
end

#gap_lengths ⇒ Object

Returns the value of attribute gap_lengths.



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# File 'lib/assembly/connection_interpreter.rb', line 301

def gap_lengths
  @gap_lengths
end

Instance Method Details

#circular? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/assembly/connection_interpreter.rb', line 304

def circular?
  @circular
end

#sequence(sequence_id_to_nucleotides_hash) ⇒ Object 



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# File 'lib/assembly/connection_interpreter.rb', line 313

def sequence(sequence_id_to_nucleotides_hash)
  raise "Programming error" unless @contigs.length == @gap_lengths.length + 1
  parts = []

  add_sequence_of = lambda do |contig|
    seq = sequence_id_to_nucleotides_hash[contig.sequence_index]
    if contig.direction == true
      parts.push seq
    elsif contig.direction == false
      parts.push Bio::Sequence::NA.new(seq).reverse_complement.to_s.upcase
    else
      raise "Programming error"
    end
  end

  add_sequence_of.call @contigs[0]

  @gap_lengths.each_with_index do |gap_length, i|
    parts.push 'N'*gap_length
    add_sequence_of.call @contigs[i+1]
  end
  return parts.join('')
end