Class: MiGA::Cli::Action::DerepWf

Inherits:
MiGA::Cli::Action show all
Includes:
Wf
Defined in:
lib/miga/cli/action/derep_wf.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 included from Wf

#call_cli, #cleanup, #create_project, #default_opts_for_wf, #download_datasets, #import_datasets, #initialize_empty_project, #opts_for_wf, #opts_for_wf_distances, #run_daemon, #summarize, #transfer_metadata

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/derep_wf.rb', line 10

def parse_cli
  default_opts_for_wf
  cli.defaults = {
    metric: :ani, threshold: 95.0, criterion: :quality,
    summaries: true, collection: true
  }
  cli.parse do |opt|
    opt.on(
      '--aai',
      'Use Average Amino Acid Identity (AAI) as genome similarity metric',
      'By default: Use Average Nucleotide Identity (ANI)'
    ) { cli[:metric] = :aai }
    opt.on(
      '--ani',
      'Use Average Nucleotide Identity (ANI) as similarity metric (default)'
    ) { cli[:metric] = :ani }
    opt.on(
      '--threshold FLOAT', Float,
      "Metric threshold (%) to dereplicate. By default: #{cli[:threshold]}"
    ) { |v| cli[:threshold] = v }
    opt.on(
      '--quality',
      'Use genome with highest quality as clade representatives (default)'
    ) { |v| cli[:criterion] = :quality }
    opt.on(
      '--medoids',
      'Use medoids as clade representatives'
    ) { |v| cli[:criterion] = :medoids }
    opt.on(
      '--no-collection',
      'Do not generate a dereplicated collection of assemblies'
    ) { |v| cli[:collection] = v }
    opt.on(
      '--no-summaries',
      'Do not generate intermediate step summaries'
    ) { |v| cli[:summaries] = v }
    opts_for_wf_distances(opt)
    opts_for_wf(opt, 'Input genome assemblies (nucleotides, FastA)')
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/derep_wf.rb', line 51

def perform
  # Input data
  p = create_project(
    :assembly,
    { run_clades: false },
    { run_mytaxa_scan: false, run_ssu: false }
  )
  p.set_option(:gsp_metric, cli[:metric].to_s)
  p.set_option(:"gsp_#{cli[:metric]}", cli[:threshold])

  # Run
  run_daemon
  dereplicate(p)
  summarize(%w[cds assembly essential_genes]) if cli[:summaries]
  cleanup
end