Method: Bio::Sequence::Common#window_search

Defined in:

lib/bio/sequence/common.rb

#window_search(window_size, step_size = 1) ⇒ Object

This method steps through a sequences in steps of ‘step_size’ by subsequences of ‘window_size’. Typically used with a block. Any remaining sequence at the terminal end will be returned.

Prints average GC% on each 100bp

s.window_search(100) do |subseq|
  puts subseq.gc
end

Prints every translated peptide (length 5aa) in the same frame

s.window_search(15, 3) do |subseq|
  puts subseq.translate
end

Split genome sequence by 10000bp with 1000bp overlap in fasta format

i = 1
remainder = s.window_search(10000, 9000) do |subseq|
  puts subseq.to_fasta("segment #{i}", 60)
  i += 1
end
puts remainder.to_fasta("segment #{i}", 60)

---

Arguments:

• (required) window_size: Fixnum

• (optional) step_size: Fixnum (default 1)

Returns

new Bio::Sequence::NA/AA object

# File 'lib/bio/sequence/common.rb', line 179

def window_search(window_size, step_size = 1)
  last_step = 0
  0.step(self.length - window_size, step_size) do |i| 
    yield self[i, window_size]                        
    last_step = i
  end                          
  return self[last_step + window_size .. -1] 
end