Class: Assemblotron::Sample

Inherits:
Object
  • Object
show all
Defined in:
lib/assemblotron/sample.rb

Instance Method Summary collapse

Constructor Details

#initialize(left, right) ⇒ Sample

Return a new Sample with left and right reads



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# File 'lib/assemblotron/sample.rb', line 8

def initialize(left, right)
  @left = left
  @right = right
end

Instance Method Details

#subsample(n, seed = 1337) ⇒ Object

Take a uniform random subsample of n reads from each of the input FASTQ files @left and @right using reservoir sampling. Return an array of length 2, containing the paths to the left and right subsampled read files.



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# File 'lib/assemblotron/sample.rb', line 134

def subsample(n, seed = 1337)
  ldir = File.dirname(@left)
  loutfile = File.join(ldir, "subset.#{File.basename @left}")

  rdir = File.dirname(@right)
  routfile = File.join(rdir, "subset.#{File.basename @right}")

  subsampleC(n, seed, @left, @right, loutfile, routfile)

  puts "Subsampled #{n} reads. Sampled read files:\n#{loutfile}\n#{routfile}"

  [loutfile, routfile]
end