Class: Bio::Velvet::Underground::Runner

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-velvet_underground/runner.rb

Class Method Summary collapse

Class Method Details

.run(kmer, velveth_options, velvetg_options = [], options = {}) ⇒ Object

Run velveth and velvetg, selecting the most memory efficient library for the purpose

kmer size: (integer) velvet_directory: where to run velvet velveth_options_string: Array of string options to velveth as on the cmdline, excluding the directory and kmer velvetg_options_string: Array of string options to velveth as on the cmdline, excluding the directory options: other options: :velvet_directory: where to run the velvets. Required (currently).



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# File 'lib/bio-velvet_underground/runner.rb', line 11

def self.run(kmer, velveth_options, velvetg_options=[], options={})
  #load library with appropriate kmer size
  Bio::Velvet::Underground.attach_shared_library(:kmer => kmer)

  velvet_directory = options[:velvet_directory]
  raise "Need options[:velvet_directory] to run velvet" if velvet_directory.nil?

  # velveth
  # Can't just pass a regular Ruby array of strings, as explained at
  # http://zegoggl.es/2009/05/ruby-ffi-recipes.html
  velveth_array_of_strings = []
  velveth_array_of_strings << FFI::MemoryPointer.from_string('velveth')
  velveth_array_of_strings << FFI::MemoryPointer.from_string(velvet_directory)
  velveth_array_of_strings << FFI::MemoryPointer.from_string(kmer.to_s)
  velveth_options.each do |o|
    velveth_array_of_strings << FFI::MemoryPointer.from_string(o)
  end
  velveth_array_of_strings << nil
  argv = FFI::MemoryPointer.new(:pointer, velveth_array_of_strings.length)
  velveth_array_of_strings.each_with_index do |p, i|
    argv[i].put_pointer(0,  p)
  end
  returned = Bio::Velvet::Underground.velveth velveth_array_of_strings.length-1, argv
  raise "Error running velveth (#{returned})" unless returned == 0

  # velvetg
  velvetg_array_of_strings = []
  velvetg_array_of_strings << FFI::MemoryPointer.from_string('velvetg')
  velvetg_array_of_strings << FFI::MemoryPointer.from_string(velvet_directory)
  velvetg_options.each do |o|
    velvetg_array_of_strings << FFI::MemoryPointer.from_string(o)
  end
  velvetg_array_of_strings << nil
  argv = FFI::MemoryPointer.new(:pointer, velvetg_array_of_strings.length)
  velvetg_array_of_strings.each_with_index do |p, i|
    argv[i].put_pointer(0,  p)
  end
  returned = Bio::Velvet::Underground.velvetg velvetg_array_of_strings.length-1, argv
  raise "Error running velvetg (#{returned})" unless returned == 0

  return 0
end