Class: Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant

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

Constant Summary collapse

INSERT =

Types:

:insert
DELETION = 
:deletion
SWAP =

n bases swapped for another n bases

:swap

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(position = nil, sequence_or_deletion_length = nil, type = nil) ⇒ Variant

Returns a new instance of Variant.



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# File 'lib/assembly/contig_printer.rb', line 346

def initialize(position=nil, sequence_or_deletion_length=nil, type=nil)
  @position = position
  @type = type
  if type == DELETION
    @deletion_length = sequence_or_deletion_length
  else
    @sequence = sequence_or_deletion_length
  end
end

Instance Attribute Details

#deletion_length ⇒ Object

length of deletion (or nil if not a deletion)



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# File 'lib/assembly/contig_printer.rb', line 341

def deletion_length
  @deletion_length
end

#position ⇒ Object

0-based position on the contig



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

def position
  @position
end

#reference_name ⇒ Object

Returns the value of attribute reference_name.



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# File 'lib/assembly/contig_printer.rb', line 332

def reference_name
  @reference_name
end

#sequence ⇒ Object

sequence (or nil if variant is a deletion)



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# File 'lib/assembly/contig_printer.rb', line 338

def sequence
  @sequence
end

#type ⇒ Object

See constants in this class



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# File 'lib/assembly/contig_printer.rb', line 344

def type
  @type
end

Instance Method Details

#base_number ⇒ Object 



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# File 'lib/assembly/contig_printer.rb', line 356

def base_number
  @position+1
end

#reverse! ⇒ Object

The reference sequence has been reverse complemented. Fix this variant so it makes sense again (position aside)



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# File 'lib/assembly/contig_printer.rb', line 374

def reverse!
  if type == SWAP or type == INSERT
    @sequence = Bio::Sequence::NA.new(@sequence).reverse_complement.to_s.upcase
  end
end

#to_shorthand ⇒ Object 



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# File 'lib/assembly/contig_printer.rb', line 360

def to_shorthand
  if type == DELETION
    "#{base_number}D:#{deletion_length}"
  elsif type == SWAP
    "#{base_number}S:#{sequence.upcase}"
  elsif type == INSERT
    "#{base_number}I:#{sequence.upcase}"
  else
    raise
  end
end

#vcf(reference_sequence) ⇒ Object 



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# File 'lib/assembly/contig_printer.rb', line 407

def vcf(reference_sequence)
  vcf_array(reference_sequence).join("\t")
end

#vcf_array(reference_sequence) ⇒ Object

CHROM POS ID REF ALT QUAL FILTER INFO



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# File 'lib/assembly/contig_printer.rb', line 381

def vcf_array(reference_sequence)
  bits = [
    @reference_name,
    @position+1,
    '.',
    ]
  case type
  when SWAP then
    bits.push reference_sequence[@position...(@position+@sequence.length) ]
    bits.push @sequence
  when INSERT then
    bits.push '.'
    bits.push @sequence
  when DELETION then
    bits.push reference_sequence[@position...(@position+@deletion_length) ]
    bits.push '.'
  else
    raise
  end

    bits.push '20'
    bits.push 'PASS'
    bits.push 'finishm'
    return bits
end