Class: Bio::FinishM::ScaffoldBreaker::Scaffold

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#contigs ⇒ Object

unscaffolded contigs from this scaffold, as an array in sorted order.



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# File 'lib/assembly/scaffold_breaker.rb', line 31

def contigs
  @contigs
end

#name ⇒ Object

Name of sequence found in the fasta file



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# File 'lib/assembly/scaffold_breaker.rb', line 34

def name
  @name
end

Instance Method Details

#contig_number(contig) ⇒ Object

Which contig number is this, in the scaffold?



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# File 'lib/assembly/scaffold_breaker.rb', line 72

def contig_number(contig)
  @contigs.each_with_index do |current_contig, i|
    return i if contig==current_contig
  end
  raise "Contig not found in scaffold"
end

#gaps ⇒ Object

Return an array of Gap objects



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# File 'lib/assembly/scaffold_breaker.rb', line 37

def gaps
  gaps = []
  last_contig = nil
  @contigs.each_with_index do |contig, i|
    if i!=0
      gap = Bio::FinishM::ScaffoldBreaker::Gap.new
      gap.scaffold = self
      gap.start = last_contig.scaffold_position_end + 1
      gap.stop = contig.scaffold_position_start - 1
      gap.number = i-1
      gaps.push gap
    end
    last_contig = contig
  end
  return gaps
end

#sequence ⇒ Object 



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# File 'lib/assembly/scaffold_breaker.rb', line 54

def sequence
  to_return = []
  last_contig = nil
  @contigs.each_with_index do |contig, i|
    if i==0
      to_return.push contig.sequence
    else
      gap_start = last_contig.scaffold_position_end + 1
      gap_stop = contig.scaffold_position_start - 1
      to_return.push 'N'*(gap_stop-gap_start+1)
      to_return.push contig.sequence
    end
    last_contig = contig
  end
  return to_return.join
end