Class: MiGA::Cli::Action::Relatives

Inherits:
MiGA::Cli::Action show all
Defined in:
lib/miga/cli/action/relatives.rb

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Attributes included from MiGA::Common::Net

#remote_connection_uri

Instance Method Summary collapse

Methods inherited from MiGA::Cli::Action

#complete, #empty_action, #initialize, #launch, load, #name

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

#download_file_ftp, #http_request, #known_hosts, #main_server, #net_method, #normalize_encoding, #remote_connection

Methods included from MiGA::Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Instance Method Details

#parse_cli ⇒ Object 



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# 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

#perform ⇒ Object 



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# 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