Class: Seqtk::Seqtk

Inherits:
Object
  • Object
show all
Includes:
Which
Defined in:
lib/seqtkrb.rb,
lib/seqtkrb/sample.rb

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Seqtk

Returns a new instance of Seqtk.



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# File 'lib/seqtkrb.rb', line 12

def initialize

  # check seqtk is installed - install it if not
  gem_dir = Gem.loaded_specs['seqtkrb'].full_gem_path
  gem_deps = File.join(gem_dir, 'deps.yaml')
  Bindeps.require gem_deps

  missing = Bindeps.missing gem_deps
  unless missing.empty?
    raise StandardError.new('seqtk was not found and ' +
                            'could not be installed')
  end

  @bin = which('seqtk').first

end

Instance Method Details

#run(cmd) ⇒ Object 



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# File 'lib/seqtkrb.rb', line 29

def run cmd

  task = Cmd.new "#{@bin} #{cmd}"
  task.run

  unless task.status.success?
    msg = "seqtk command #{cmd} failed\n"
    msg << "stdout:\n"
    msg << task.stdout
    msg << "\nstderr:\n"
    msg << task.stderr
    raise StandardError.new(msg)
  end

end

#sample(infile, outfile, n, seed = -1)) ⇒ Object 



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# File 'lib/seqtkrb/sample.rb', line 5

def sample(infile, outfile, n, seed=-1)
  run "sample #{seedstr seed} #{infile} #{n} > #{outfile}"
end

#sample_lowmem(infile, outfile, n, seed = -1)) ⇒ Object 



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# File 'lib/seqtkrb/sample.rb', line 9

def sample_lowmem(infile, outfile, n, seed=-1)
  run "sample -2 #{seedstr seed} #{infile} #{n} > #{outfile}"
end

#seedstr(seed) ⇒ Object 



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# File 'lib/seqtkrb/sample.rb', line 13

def seedstr seed
  seed == -1 ? "" : "-s #{seed}"
end