Class: Bio::Velvet::Runner

Inherits:
Object
  • Object
show all
Includes:
Logging, Parallel::ProcessorCount
Defined in:
lib/bio-velvet/runner.rb

Instance Method Summary collapse

Methods included from Logging

#log

Instance Method Details

#binary_version(velveth_path = 'velveth') ⇒ Object

Detect the binary version currently in use and return as a String



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# File 'lib/bio-velvet/runner.rb', line 85

def binary_version(velveth_path='velveth')
  cmd = velveth_path
  log.info "Running velveth: #{cmd}" if log.info?
  status, stdout, stderr = systemu cmd
  if status.exitstatus != 0
    raise VelvetRunnerException, "Error running velveth: #{stderr}\n#{stdout}"
  end
  splits = stdout.split("\n")
  if splits.length > 1 and matches = splits[1].match(/^Version (.+)$/)
    return matches[1]
  else
    raise "Unable to parse the version number from running `#{cmd}', the output was: #{stdout}"
  end
end

#set_num_cpus(num_cpus = nil) ⇒ Object

According to the manual, “Velvet will the use up to OMP_NUM_THREADS+1 or OMP_THREAD_LIMIT threads.”

Argument is the number of CPUs, or nil if all CPUs on the machine are to be used



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# File 'lib/bio-velvet/runner.rb', line 105

def set_num_cpus(num_cpus=nil)
  num_cpus ||= processor_count #from the parallel gem
  log.debug "Setting number of CPUs to run velvet with to #{num_cpus}."
  ENV['OMP_NUM_THREADS'] = (num_cpus - 1).to_s
  ENV['OMP_THREAD_LIMIT'] = num_cpus.to_s
end

#velvet(kmer_length, velveth_options_string, velvetg_options_string = '', options = {}) ⇒ Object

Run velveth and then velvetg, with the given kmer size. Returned is a Bio::Velvet::Result class, stored in a temporary directory. The temporary directory is removed upon program exit.

The velveth_options and velvetg_options are strings to pass as arguments to velveth and velvetg, respectively.

The final options argument is used to specify bio-velvet wrapper options. Currently: :output_assembly_path: a directory where the assembly takes place [default: a temporary directory] :velveth_path: path to the velveth binary [default: ‘velveth’] :velvetg_path: path to the velvetg binary [default: ‘velvetg’] :threads: number of threads to use [default: all threads on the machine]



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# File 'lib/bio-velvet/runner.rb', line 23

def velvet(kmer_length, velveth_options_string, velvetg_options_string='', options={})
  res = velveth kmer_length, velveth_options_string, options
  velvetg res, velvetg_options_string, options
end

#velvetg(velveth_result_object, velvetg_arguments, options = {}) ⇒ Object

Run velvetg, with a Bio::Velvet::Result object generated with velveth, and velvetg arguments as a String (no need to specify the velvet directory, just the extra arguments).

Further options (the third argument): :velvetg_path: path to the velvetg binary [default: ‘velvetg’]



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# File 'lib/bio-velvet/runner.rb', line 66

def velvetg(velveth_result_object, velvetg_arguments, options={})
  binary = options[:velvetg_path]
  binary ||= 'velvetg'

  cmd = "#{binary} #{velveth_result_object.result_directory} #{velvetg_arguments}"

  log.info "Running velvetg: #{cmd}" if log.info?
  status, stdout, stderr = systemu cmd
  if status.exitstatus != 0
    raise VelvetRunnerException, "Error running velvetg: #{stderr}\n#{stdout}"
  end
  velveth_result_object.velvetg_stdout = stdout
  velveth_result_object.velvetg_stderr = stderr

  return velveth_result_object
end

#velveth(kmer_length, velveth_arguments, options = {}) ⇒ Object

Run velveth with the given kmer and return a Bio::Velvet::Result object

Options: :velveth_path: path to the velveth binary [default: ‘velveth’]



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# File 'lib/bio-velvet/runner.rb', line 32

def velveth(kmer_length, velveth_arguments, options={})
  set_num_cpus(options[:threads])
  result = Result.new
  outdir = nil
  if options[:output_assembly_path]
    log.debug "Using pre-defined assembly directory: #{options[:output_assembly_path] }"
    outdir = options[:output_assembly_path]
  else
    outdir = Files.create.root
  end
  result.result_directory = outdir

  binary = options[:velveth_path]
  binary ||= 'velveth'

  # Run velveth
  cmd = "#{binary} #{result.result_directory} #{kmer_length} #{velveth_arguments}"
  log.info "Running velveth: #{cmd}" if log.info?
  status, stdout, stderr = systemu cmd
  if status.exitstatus != 0
    raise VelvetRunnerException, "Error running velveth: #{stderr}\n#{stdout}"
  end
  result.velveth_stdout = stdout
  result.velveth_stderr = stderr

  return result
end