class MiGA::Cli::Action::Relatives

# File lib/miga/cli/action/relatives.rb, line 7
def parse_cli
  cli.defaults = { metric: :aai, external: false, how_many: 5 }
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset_opt])
    cli.opt_filter_datasets(opt)
    opt.on(
      '--metric STRING',
      'Use this metric of identity, one of ANI or AAI (default)'
    ) { |v| cli[:metric] = v.downcase.to_sym }
    opt.on(
      '--ref-project',
      'Report distances to the external reference project used for taxonomy',
      'By default: report distances to other datasets in the project'
    ) { |v| cli[:external] = v }
    opt.on(
      '-n', '--how-many INT', Integer,
      'Number of top values to report'
    ) { |v| cli[:how_many] = v }
    opt.on(
      '--tab',
      'Return a tab-delimited table'
    ) { |v| cli[:tabular] = v }
    opt.on(
      '-o', '--output PATH',
      'Create output file instead of returning to STDOUT'
    ) { |v| cli[:output] = v }
  end
end

# File lib/miga/cli/action/relatives.rb, line 36
def perform
  cr = []
  cli.load_and_filter_datasets.each do |d|
    d_cr = d.closest_relatives(cli[:how_many], cli[:external], cli[:metric])
    d_cr ||= []
    cr += d_cr.map { |i| [d.name] + i }
  end
  io = cli[:output].nil? ? $stdout : File.open(cli[:output], 'w')
  cli.table(['dataset_A', 'dataset_B', cli[:metric]], cr, io)
end