Class: Bio::Velvet::Graph::Node

Inherits:
Object
  • Object
show all
Includes:
Logging
Defined in:
lib/bio-velvet/graph.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Logging

#log

Instance Attribute Details

#coverages ⇒ Object

Returns the value of attribute coverages.



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# File 'lib/bio-velvet/graph.rb', line 379

def coverages
  @coverages
end

#ends_of_kmers_of_node ⇒ Object

Returns the value of attribute ends_of_kmers_of_node.



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# File 'lib/bio-velvet/graph.rb', line 379

def ends_of_kmers_of_node
  @ends_of_kmers_of_node
end

#ends_of_kmers_of_twin_node ⇒ Object

Returns the value of attribute ends_of_kmers_of_twin_node.



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# File 'lib/bio-velvet/graph.rb', line 379

def ends_of_kmers_of_twin_node
  @ends_of_kmers_of_twin_node
end

#length ⇒ Object

Number of nucleotides in this node if a contig was made from this contig alone



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# File 'lib/bio-velvet/graph.rb', line 390

def length
  @length
end

#node_id ⇒ Object

Returns the value of attribute node_id.



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# File 'lib/bio-velvet/graph.rb', line 379

def node_id
  @node_id
end

#number_of_short_reads ⇒ Object

For read tracking



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# File 'lib/bio-velvet/graph.rb', line 382

def number_of_short_reads
  @number_of_short_reads
end

#parent_graph ⇒ Object

Graph to which this node belongs



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# File 'lib/bio-velvet/graph.rb', line 387

def parent_graph
  @parent_graph
end

#short_reads ⇒ Object

For read tracking - an array of NodedRead objects



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# File 'lib/bio-velvet/graph.rb', line 384

def short_reads
  @short_reads
end

Instance Method Details

#corresponding_contig_length ⇒ Object

The common length of [ends_of_kmers_of_node and :ends_of_kmers_of_twin_node] is equal to the length of the corresponding contig minus k − 1.

This method returns that corresponding contig’s length



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# File 'lib/bio-velvet/graph.rb', line 424

def corresponding_contig_length
  @ends_of_kmers_of_node.length+@parent_graph.hash_length-1
end

#coverage ⇒ Object

Return the sum of all coverage columns, divided by the length of the node, or nil if this node has no coverage



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# File 'lib/bio-velvet/graph.rb', line 459

def coverage
  return nil if length == 0

  coverage = 0
  coverages.each_with_index do |cov, i|
    # Only take the 0th, 2nd, 4th, etc, don't want the O_cov things
    coverage += cov if i.modulo(2) == 0
  end
  return coverage.to_f / length
end

#inspect ⇒ Object 



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# File 'lib/bio-velvet/graph.rb', line 453

def inspect
  to_s
end

#length_alone ⇒ Object

Number of nucleotides in this node if this contig length is being added to another node’s length (nodes overlap)



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# File 'lib/bio-velvet/graph.rb', line 416

def length_alone
  @ends_of_kmers_of_node.length
end

#reverse_sequence ⇒ Object

The reverse complement of this node’s sequence



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# File 'lib/bio-velvet/graph.rb', line 439

def reverse_sequence
  revcom(sequence)
end

#sequence ⇒ Object

The sequence of this node, should a contig be made solely out of this node. The kmer length is that kmer length that was used to create the assembly.

If this node has a sequence that is 2 or more less than the hash length, then the sequence of this node requires information outside of this object, and gathering that information is not implemented here.



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# File 'lib/bio-velvet/graph.rb', line 398

def sequence
  if !sequence?
    raise NotImplementedException, "Attempted to get the sequence of a velvet node that is too short, such that the sequence info is not fully present in the node object"
  end
  kmer_length = @parent_graph.hash_length

   # Sequence is the reverse complement of the ends_of_kmers_of_twin_node,
   # Then the ends_of_kmers_of_node after removing the first kmer_length - 1
   # nucleotides
   length_to_get_from_fwd = corresponding_contig_length - @ends_of_kmers_of_twin_node.length
   fwd_length = @ends_of_kmers_of_node.length
   raise "Programming error" if length_to_get_from_fwd > fwd_length
   revcom(@ends_of_kmers_of_twin_node)+
     @ends_of_kmers_of_node[-length_to_get_from_fwd...fwd_length]
end

#sequence? ⇒ Boolean

Is it possible to extract the sequence of this node? I.e. is it long enough?

Returns:

  • (Boolean) 


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# File 'lib/bio-velvet/graph.rb', line 429

def sequence?
  kmer_length = @parent_graph.hash_length
  if kmer_length -1 > @ends_of_kmers_of_node.length
    return false
  else
    return true
  end
end

#to_s ⇒ Object 



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# File 'lib/bio-velvet/graph.rb', line 443

def to_s
  fwd = @ends_of_kmers_of_node
  rev = @ends_of_kmers_of_twin_node
  if @ends_of_kmers_of_node.length > 10
    fwd = @ends_of_kmers_of_node[0...10]+'..'
    rev = @ends_of_kmers_of_twin_node[0...10]+'..'
  end
  "Node from #{@parent_graph.class}: #{@node_id}: #{fwd} / #{rev}"
end