Class: Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/assembly/bubbly_assembler.rb

Constant Summary collapse

DIVERGES_FATE = 
'diverges'
DEAD_END_FATE = 
'dead end'
CIRCUIT_FATE = 
'circuit'
NODE_COUNT_LIMIT_REACHED = 
'too many nodes in bubble'

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ MetaPath

Returns a new instance of MetaPath.



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# File 'lib/assembly/bubbly_assembler.rb', line 335

def initialize
  @internal_array = []
end

Instance Attribute Details

#fate ⇒ Object

How does this metapath end?



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# File 'lib/assembly/bubbly_assembler.rb', line 331

def fate
  @fate
end

Instance Method Details

#<<(oriented_node_or_bubble) ⇒ Object Also known as: push 



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# File 'lib/assembly/bubbly_assembler.rb', line 367

def <<(oriented_node_or_bubble)
  @internal_array << oriented_node_or_bubble
end

#[](index) ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 345

def [](index)
  @internal_array[index]
end

#coverage ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 436

def coverage
  coverages = []
  lengths = []
  each do |onode_or_bubble|
    if onode_or_bubble.kind_of?(Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble)
      # Length isn't obvious, but let's go with reference path length just coz that's easy
      this_length = onode_or_bubble.reference_trail.length_in_bp_within_path
      lengths.push this_length

      # Coverage of a bubble is the coverage of each node in the bubble
      # each weighted by their length
      coverages.push onode_or_bubble.coverage
    else
      #regular node. So simple average coverage
      coverages.push onode_or_bubble.node.coverage
      lengths.push onode_or_bubble.node.length_alone
    end
  end

  # Then a simple weighted average
  i = -1
  total_length = lengths.reduce(:+)

  answer =  coverages.reduce(0.0) do |sum, cov|
    i += 1
    sum + (cov * lengths[i].to_f / total_length)
  end
  answer
end

#delete_at(index) ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 349

def delete_at(index)
  @internal_array.delete_at index
end

#each ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 339

def each
  @internal_array.each do |e|
    yield e
  end
end

#each_oriented_node ⇒ Object

bits.



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# File 'lib/assembly/bubbly_assembler.rb', line 394

def each_oriented_node
  @internal_array.each do |e|
    if e.kind_of?(Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble)
      e.oriented_nodes.each do |onode|
        yield onode
      end
    else
      yield e
    end
  end
end

#empty? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/assembly/bubbly_assembler.rb', line 353

def empty?
  @internal_array.empty?
end

#last_oriented_node ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 357

def last_oriented_node
  e = @internal_array[-1]
  if e.kind_of?(Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode)
    return e
  else
    # it is a bubble
    return e.converging_oriented_node
  end
end

#length ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 388

def length
  @internal_array.length
end

#length_in_bp ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 406

def length_in_bp
  sum = 0
  each do |e|
    if e.kind_of?(Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble)
      sum += e.reference_trail.length_in_bp_within_path
    else
      sum += e.node.length_alone
    end
  end
  return sum
end

#reference_trail ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 418

def reference_trail
  trail = Bio::Velvet::Graph::OrientedNodeTrail.new

  trail.trail = collect do |e|
    if e.kind_of?(Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble)
      e.reference_trail.trail
    else
      e
    end
  end.flatten

  return trail
end

#reverse! ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 376

def reverse!
  # Do regular reversal
  @internal_array.reverse!

  # Reverse all the internal parts
  @internal_array.each do |e|
    e.reverse!
  end

  return nil
end

#sequence ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 432

def sequence
  reference_trail.sequence
end

#to_shorthand ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 372

def to_shorthand
  @internal_array.collect{|e| e.to_shorthand}.join(',')
end